Main Page

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    <comment>Original page content from 07-Jan-2007</comment>
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    <text bytes="1425" xml:space="preserve">This [http://en.wikipedia.org/wiki/Wiki wiki] is a community effort to document the [http://refbase.sourceforge.net/ refbase] web application.

== About refbase ==

[http://refbase.sourceforge.net/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[refbase:Community_Portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

== Users of Refbase ==
[[Refbase User|Several institutions]] around the world are using refbase. If you maintain your own publicly available installation, you're welcome to add it to the list!


__NOTOC__
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    <timestamp>2023-10-24T13:19:39Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update SourceForge forum links</comment>
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    <text bytes="1445" xml:space="preserve">This [http://en.wikipedia.org/wiki/Wiki wiki] is a community effort to document the [https://sourceforge.net/projects/refbase/ refbase] web application.

== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[refbase:Community_Portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

== Users of Refbase ==
[[Refbase User|Several institutions]] around the world are using refbase. If you maintain your own publicly available installation, you're welcome to add it to the list!


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    <minor/>
    <comment>Update link to Community_Portal page</comment>
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    <text bytes="1454" xml:space="preserve">This [http://en.wikipedia.org/wiki/Wiki wiki] is a community effort to document the [https://sourceforge.net/projects/refbase/ refbase] web application.

== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[wiki.refbase.net:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

== Users of Refbase ==
[[Refbase User|Several institutions]] around the world are using refbase. If you maintain your own publicly available installation, you're welcome to add it to the list!


__NOTOC__
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    <contributor>
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    <comment>Remove excessive whitespace below page content</comment>
    <model>wikitext</model>
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    <text bytes="1453" xml:space="preserve">This [http://en.wikipedia.org/wiki/Wiki wiki] is a community effort to document the [https://sourceforge.net/projects/refbase/ refbase] web application.

== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[wiki.refbase.net:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

== Users of Refbase ==
[[Refbase User|Several institutions]] around the world are using refbase. If you maintain your own publicly available installation, you're welcome to add it to the list!

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    <comment>Add "refbase" badge at top of page</comment>
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&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt;
&lt;/div&gt;


This [http://en.wikipedia.org/wiki/Wiki wiki] is a community effort to document the [https://sourceforge.net/projects/refbase/ refbase] web application.

== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[wiki.refbase.net:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

== Users of Refbase ==
[[Refbase User|Several institutions]] around the world are using refbase. If you maintain your own publicly available installation, you're welcome to add it to the list!

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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Removes first sentence and, for now, the "Users of Refbase" section</comment>
    <model>wikitext</model>
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    <text bytes="1173" xml:space="preserve">&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt;
&lt;/div&gt;


== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[wiki.refbase.net:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

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    <id>48</id>
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    <timestamp>2023-10-26T10:42:36Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Adds a "Download" section</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1670" xml:space="preserve">&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt;
&lt;/div&gt;


== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Download ==

You can [https://sourceforge.net/projects/refbase/files/latest/download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [https://sourceforge.net/p/refbase/code checked out] and [[SVN_version|installed]] from the refbase Subversion repository.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[wiki.refbase.net:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

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      <id>1</id>
    </contributor>
    <minor/>
    <comment>Correct link to refbase community portal</comment>
    <model>wikitext</model>
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    <text bytes="1661" xml:space="preserve">&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt;
&lt;/div&gt;


== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

== Download ==

You can [https://sourceforge.net/projects/refbase/files/latest/download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [https://sourceforge.net/p/refbase/code checked out] and [[SVN_version|installed]] from the refbase Subversion repository.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[refbase:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

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<page arvcontinue="">
  <title>Web Reference Database</title>
  <ns>0</ns>
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    <id>3</id>
    <timestamp>2023-10-23T17:42:42Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 20-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2800" xml:space="preserve">&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt; &lt;br /&gt; 
'''web-based, platform-independent, &lt;br /&gt; multi-user interface for managing &lt;br /&gt; scientific literature &amp; citations'''
&lt;/div&gt;

== Features ==

refbase can import and export references in various formats (including BibTeX, Endnote, RIS, PubMed, ISI Web of Science, CSA Illumina, RefWorks, MODS XML, OpenOffice, and MS Word). It can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers powerful searching, and RSS support. Its OpenSearch and SRU/W web services, and support for unAPI &amp; COinS metadata allow for easy access by clients and search engines. Please see our [[Feature highlights]] page for a more detailed description of features. An overview of the major feature additions in refbase-0.9.5 is given [[Main_features#refbase-0.9.5|here]].

== Download ==

You can [http://prdownloads.sourceforge.net/refbase/refbase-0.9.5.tar.gz?download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [http://sourceforge.net/svn/?group_id=64647 checked out] and [[SVN_version|installed]] from the refbase [http://refbase.svn.sourceforge.net/viewvc/refbase/ Subversion repository].
&lt;div id="top-right-floater"&gt;&lt;div id="direct-download-link"&gt;'''[http://prdownloads.sourceforge.net/refbase/refbase-0.9.5.tar.gz?download Download&lt;br /&gt;refbase 0.9.5]'''&lt;/div&gt;&lt;/div&gt;

== Demo &amp; Documentation ==

We invite you to test-drive refbase at the [http://demo.refbase.net/ refbase Demo Database] (latest stable release version) or the [http://beta.refbase.net/ refbase Beta Database] (latest development version). Feel free to login and play around! Further demo and real-world installations are listed [[Refbase_users|here]]. For available documentation, useful tips and troubleshooting guidance, please see the main [[Documentation]] page.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the [[Documentation|docs]], want to discuss new or existing features or want to get involved with the ongoing development of refbase please see our [[Refbase:Community_Portal|Community Portal]] for pointers to forums, mailing lists and contact information.

&lt;div id="bottom-right-floater"&gt;&lt;div id="contact"&gt;Contact: &lt;br /&gt; [mailto:info@refbase.net Matthias Steffens &amp;amp; &lt;br /&gt; Richard Karnesky]&lt;/div&gt;&lt;div id="bibliophile-credit"&gt;Member of [http://bibliophile.sourceforge.net/ Bibliophile]&lt;/div&gt;&lt;div id="sourceforge-credit"&gt;[http://sourceforge.net/projects/refbase/ Project Home] &lt;br /&gt; Hosted by [http://www.sourceforge.net SourceForge]&lt;/div&gt;&lt;/div&gt;
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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Removes info that was previously displayed in a sidebar (which is partly outdated &amp; won't work on mobile)</comment>
    <model>wikitext</model>
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&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt; &lt;br /&gt; 
'''web-based, platform-independent, &lt;br /&gt; multi-user interface for managing &lt;br /&gt; scientific literature &amp; citations'''
&lt;/div&gt;

== Features ==

refbase can import and export references in various formats (including BibTeX, Endnote, RIS, PubMed, ISI Web of Science, CSA Illumina, RefWorks, MODS XML, OpenOffice, and MS Word). It can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers powerful searching, and RSS support. Its OpenSearch and SRU/W web services, and support for unAPI &amp; COinS metadata allow for easy access by clients and search engines. Please see our [[Feature highlights]] page for a more detailed description of features. An overview of the major feature additions in refbase-0.9.5 is given [[Main_features#refbase-0.9.5|here]].

== Download ==

You can [http://prdownloads.sourceforge.net/refbase/refbase-0.9.5.tar.gz?download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [http://sourceforge.net/svn/?group_id=64647 checked out] and [[SVN_version|installed]] from the refbase [http://refbase.svn.sourceforge.net/viewvc/refbase/ Subversion repository].

== Demo &amp; Documentation ==

We invite you to test-drive refbase at the [http://demo.refbase.net/ refbase Demo Database] (latest stable release version) or the [http://beta.refbase.net/ refbase Beta Database] (latest development version). Feel free to login and play around! Further demo and real-world installations are listed [[Refbase_users|here]]. For available documentation, useful tips and troubleshooting guidance, please see the main [[Documentation]] page.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the [[Documentation|docs]], want to discuss new or existing features or want to get involved with the ongoing development of refbase please see our [[Refbase:Community_Portal|Community Portal]] for pointers to forums, mailing lists and contact information.

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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update SourceForge links</comment>
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&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt; &lt;br /&gt; 
'''web-based, platform-independent, &lt;br /&gt; multi-user interface for managing &lt;br /&gt; scientific literature &amp; citations'''
&lt;/div&gt;

== Features ==

refbase can import and export references in various formats (including BibTeX, Endnote, RIS, PubMed, ISI Web of Science, CSA Illumina, RefWorks, MODS XML, OpenOffice, and MS Word). It can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers powerful searching, and RSS support. Its OpenSearch and SRU/W web services, and support for unAPI &amp; COinS metadata allow for easy access by clients and search engines. Please see our [[Feature highlights]] page for a more detailed description of features. An overview of the major feature additions in refbase-0.9.5 is given [[Main_features#refbase-0.9.5|here]].

== Download ==

You can [https://sourceforge.net/projects/refbase/files/latest/download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [https://sourceforge.net/p/refbase/code checked out] and [[SVN_version|installed]] from the refbase Subversion repository.

== Demo &amp; Documentation ==

We invite you to test-drive refbase at the [http://demo.refbase.net/ refbase Demo Database] (latest stable release version) or the [http://beta.refbase.net/ refbase Beta Database] (latest development version). Feel free to login and play around! Further demo and real-world installations are listed [[Refbase_users|here]]. For available documentation, useful tips and troubleshooting guidance, please see the main [[Documentation]] page.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the [[Documentation|docs]], want to discuss new or existing features or want to get involved with the ongoing development of refbase please see our [[Refbase:Community_Portal|Community Portal]] for pointers to forums, mailing lists and contact information.

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<page arvcontinue="">
  <title>Documentation</title>
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    <comment>Original page content from 19-Dec-2008</comment>
    <model>wikitext</model>
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    <text bytes="1774" xml:space="preserve">== General ==

* [[Main features]]
* [[Planned feature additions]]
* [[Release notes]]
* [[The 'next release' question]]
* [[Roadmap]]

== Installation ==

* [[Installing refbase]]
* [[Requirements]]
* [[Bibutils|Installing Bibutils]]
* [[Database configuration]]
* [[Creating the first user]]
* [[Updating refbase]]
* [[Installation-Troubleshooting]]
* [[Manual installation]]
* [[SVN version]]

== Configuration ==

* [[Configuring refbase]]
* [[Interface customization]]

== Usage ==

* [[Interface]]
* [[Interface FAQ]]
* [[Searching]]
* [[Editing records]]
* [[Adding records]]
* [[Deleting records]]
* [[Importing records]]
* [[Exporting records]]
* [[Sharing records]]
* [[Managing record groups]]
* Citation
** [[Citation lists]]
** [[Citation styles]]
** [[BibTeX/LaTeX integration]]
** [[MS Word integration]]
** [[OO.o Writer integration]]
* [[Integration with other reference managers]]
* [[Integration with online services]]
* [[RSS features]]
* [[Refbase markup syntax]]
* [[Placeholder syntax]]
* [[Relating records to each other]]

== Accessing data ==

* [[Linking to records]]
* [[Auto-updating author/group bibliographies]]
* [[Integrating refbase into your web site]]
* [[Standard link resolver support: OpenURL &amp; COinS]]
* [[unAPI service]]
* [[OpenSearch service]]
* [[Search/Retrieve web services]]
* [[Command line clients]]
* [[Biblio::Refbase|Biblio::Refbase Perl module]]

== Customization ==

* [[User options]]
* [[Customizing the display of results]]
* [[Customizing user authentication (Pubcookie)]]

== Administration ==

* [[User management]]
* [[Batch SQL modifications]]
* [[Handling of duplicates]]
* [[Backup the database]]

== Database information ==

* [[MySQL tables]]

== Troubleshooting ==

* [[Troubleshooting]]


[[Category:Docs]]</text>
    <sha1>9ff14e77f1dcd06fa9cbc1bb7a39e62031fdf0c1</sha1>
  </revision>
  <revision>
    <id>5</id>
    <parentid>4</parentid>
    <timestamp>2023-10-24T07:39:29Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1792" xml:space="preserve">== General ==

* [[Main features]]
* [[Planned feature additions]]
* [[Release notes]]
* [[The 'next release' question]]
* [[Roadmap]]

== Installation ==

* [[Installing refbase]]
* [[Requirements]]
* [[Bibutils|Installing Bibutils]]
* [[Database configuration]]
* [[Creating the first user]]
* [[Updating refbase]]
* [[Installation-Troubleshooting]]
* [[Manual installation]]
* [[SVN version]]

== Configuration ==

* [[Configuring refbase]]
* [[Interface customization]]

== Usage ==

* [[Interface]]
* [[Interface FAQ]]
* [[Searching]]
* [[Editing records]]
* [[Adding records]]
* [[Deleting records]]
* [[Importing records]]
* [[Exporting records]]
* [[Sharing records]]
* [[Managing record groups]]
* Citation
** [[Citation lists]]
** [[Citation styles]]
** [[BibTeX/LaTeX integration]]
** [[MS Word integration]]
** [[OO.o Writer integration]]
* [[Integration with other reference managers]]
* [[Integration with online services]]
* [[RSS features]]
* [[Refbase markup syntax]]
* [[Placeholder syntax]]
* [[Relating records to each other]]

== Accessing data ==

* [[Linking to records]]
* [[Auto-updating author/group bibliographies]]
* [[Integrating refbase into your web site]]
* [[Standard link resolver support: OpenURL &amp; COinS]]
* [[unAPI service]]
* [[OpenSearch service]]
* [[Search/Retrieve web services]]
* [[Command line clients]]
* [[Biblio::Refbase|Biblio::Refbase Perl module]]

== Customization ==

* [[User options]]
* [[Customizing the display of results]]
* [[Customizing user authentication (Pubcookie)]]

== Administration ==

* [[User management]]
* [[Batch SQL modifications]]
* [[Handling of duplicates]]
* [[Backup the database]]

== Database information ==

* [[MySQL tables]]

== Troubleshooting ==

* [[Troubleshooting]]


[[Category:Docs]]
__NOEDITSECTION__</text>
    <sha1>19866331b575fc6ec4255c34f68a208b93ed1c6c</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>MediaWiki:Sitesupport-url</title>
  <ns>8</ns>
  <id>5</id>
  <revision>
    <id>6</id>
    <timestamp>2023-10-24T11:57:10Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Created page with "https://wiki.refbase.net/refbase:Site_support"</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="45" xml:space="preserve">https://wiki.refbase.net/refbase:Site_support</text>
    <sha1>669343830a452025cfc6d03648445ed8dd1ede77</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>MediaWiki:Sitesupport</title>
  <ns>8</ns>
  <id>6</id>
  <revision>
    <id>7</id>
    <timestamp>2023-10-24T12:00:49Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Menu item title for "Donate" link</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6" xml:space="preserve">Donate</text>
    <sha1>95345e276ffbb748fffc3a9b8c9322bd0b489d39</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>refbase:General disclaimer</title>
  <ns>4</ns>
  <id>8</id>
  <revision>
    <id>9</id>
    <timestamp>2023-10-24T12:32:00Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 07-Jan-2007 (original wiki page: "refbase:General_disclaimer")</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="170" xml:space="preserve">Please note that we cannot guarantee for the quality and accuracy of the content provided by this wiki.

You expressly agree that use of the service is at your sole risk.</text>
    <sha1>c5cecbf054eb0c35d884b461bacfe28080410177</sha1>
  </revision>
</page>
<page arvcontinue="">
  <title>MediaWiki:Common.css</title>
  <ns>8</ns>
  <id>9</id>
  <revision>
    <id>10</id>
    <timestamp>2023-10-24T12:48:51Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Add CSS for Minerva skin to hide page tabs ("Project Page" &amp; "Discussion") and page actions menu</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="135" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}</text>
    <sha1>59e44ac5193c7abb007ec2056b9b802b19cfd4af</sha1>
  </revision>
  <revision>
    <id>21</id>
    <parentid>10</parentid>
    <timestamp>2023-10-24T15:15:59Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Adds a red border above the page content</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="181" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}</text>
    <sha1>9c61c38af43ac2df1697a662a733ec06a8be2e31</sha1>
  </revision>
  <revision>
    <id>22</id>
    <parentid>21</parentid>
    <timestamp>2023-10-24T15:44:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Change footer to use a dark blue background with a red border and refbase icon</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="386" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	border-top: 3px solid #990000;
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}</text>
    <sha1>2844e1873820580631d914e54e45f3149149c14d</sha1>
  </revision>
  <revision>
    <id>23</id>
    <parentid>22</parentid>
    <timestamp>2023-10-24T15:48:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Keep last modified bar in footer with original (grey) background</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="438" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	border-top: 3px solid #990000;
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	background-color: #EAECF0;
}</text>
    <sha1>4c3e3b2667c2f5c3de45f948ec3ac667e33c644b</sha1>
  </revision>
  <revision>
    <id>24</id>
    <parentid>23</parentid>
    <timestamp>2023-10-24T15:50:07Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Move red border in footer below last modified bar</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="441" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}</text>
    <sha1>04a007a1d3c4d81cf15dbff28c384bb6232fde87</sha1>
  </revision>
  <revision>
    <id>25</id>
    <parentid>24</parentid>
    <timestamp>2023-10-25T07:32:09Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Better color contrast for footer links</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="534" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}</text>
    <sha1>8af0a61a7d7e500358b4774ee004154e86436eb0</sha1>
  </revision>
  <revision>
    <id>26</id>
    <parentid>25</parentid>
    <timestamp>2023-10-25T07:35:48Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Slightly increase margin below footer links for better mobile touch experience</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="577" xml:space="preserve">/* CSS placed here will be applied to all skins */

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}</text>
    <sha1>d1d994fb7403051ff994bae2ef88fa7f3201b304</sha1>
  </revision>
  <revision>
    <id>27</id>
    <parentid>26</parentid>
    <timestamp>2023-10-25T08:12:47Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Set "refbase" wiki title in page header as bold</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="617" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}</text>
    <sha1>ab0db2409c2319455163b49197daab72dc0366a4</sha1>
  </revision>
  <revision>
    <id>28</id>
    <parentid>27</parentid>
    <timestamp>2023-10-25T08:30:32Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Use a sans-serif font family for page headings</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="685" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
}

.page-heading &gt; *, .mw-headline &gt; * {
  font-family: sans-serif;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}</text>
    <sha1>a24a4f72790d6229caf7ad6ed006089e94a24a84</sha1>
  </revision>
  <revision>
    <id>29</id>
    <parentid>28</parentid>
    <timestamp>2023-10-25T08:32:31Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Undo revision 28 by [[Special:Contributions/WikiSysop|WikiSysop]] ([[User talk:WikiSysop|talk]])</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="617" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}</text>
    <sha1>ab0db2409c2319455163b49197daab72dc0366a4</sha1>
  </revision>
  <revision>
    <id>35</id>
    <parentid>29</parentid>
    <timestamp>2023-10-25T20:54:30Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Format "refbase" name on "Web_Reference_Database" page</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="846" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}

#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}</text>
    <sha1>55cb558f80c018a23919e2e31d5f954cf564d681</sha1>
  </revision>
  <revision>
    <id>36</id>
    <parentid>35</parentid>
    <timestamp>2023-10-25T21:03:08Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>More CSS styling to facilitate the old look of the "Web_Reference_Database" page</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="1921" xml:space="preserve">/* CSS placed here will be applied to all skins */

/* CSS styling intended for the "MinervaNeue" skin (MediaWiki 1.39.3) */

.branding-box {
  font-weight: bold;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}


/* CSS styling specifically for the "Web_Reference_Database" page */

#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}

#top-right-floater {
	position: absolute;
	top: 75px;
	right: 30px;
	width: 170px;
}

#direct-download-link {
	height: 75px;
	display: block;
	background-image: url("badge.gif");
	background-repeat: no-repeat;
	background-position: right 10px;
}

#direct-download-link a {
	font-size: 90%;
	position: relative;
	top: 30px;
}

#bottom-right-floater {
	position: absolute;
	right: 20px;
	width: 165px;
	float: right;
	font-size: 80%;
}

#contact {
	position: relative;
	top: -215px;
}

#bibliophile-credit {
	position: relative;
	top: -180px;
	height: 65px;
	display: block;
	background-image: url("bibliophile_logo.gif");
	background-repeat: no-repeat;
	background-position: -2px 18px;
}

#sourceforge-credit {
	position: relative;
	top: -155px;
	height: 80px;
	display: block;
	background-image: url("http://sourceforge.net/sflogo.php?group_id=64647&amp;amp;type=1");
	background-repeat: no-repeat;
	background-position: 1px 35px;
}</text>
    <sha1>fd8522c26224bc5f608f3ed0919b24aa5d012c1c</sha1>
  </revision>
  <revision>
    <id>37</id>
    <parentid>36</parentid>
    <timestamp>2023-10-25T21:12:28Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Undo revision 36 by [[Special:Contributions/WikiSysop|WikiSysop]] ([[User talk:WikiSysop|talk]])</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="846" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
}

.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}

#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}</text>
    <sha1>55cb558f80c018a23919e2e31d5f954cf564d681</sha1>
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    <timestamp>2023-10-26T06:34:00Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Style page headings in red color, centered and slightly larger</comment>
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    <format>text/css</format>
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.branding-box {
  font-weight: bold;
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h1 { 
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.minerva__tab-container {
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}

.page-actions-menu {
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#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
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.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
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#footer-places a:link {
  color: #CCCCCC;
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#footer-places a:visited {
  color: #AAAAAA;
}

#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}</text>
    <sha1>30c983095421cb309d07d296c262c11dd61b5371</sha1>
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  <revision>
    <id>44</id>
    <parentid>43</parentid>
    <timestamp>2023-10-26T06:35:24Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Remove erroneous font-size attribute for page headings</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="893" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
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	display: none;
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.page-actions-menu {
	display: none;
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#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
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.footer-content:before{
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.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
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#footer-places {
  margin-bottom: 15px;
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#footer-places a:link {
  color: #CCCCCC;
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#footer-places a:visited {
  color: #AAAAAA;
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#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}</text>
    <sha1>97c2e99f09e3914e308a44e4562b81c881986193</sha1>
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  <revision>
    <id>45</id>
    <parentid>44</parentid>
    <timestamp>2023-10-26T06:38:06Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Color page subheadings in red</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="929" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
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h1 { 
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.mw-headline { 
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.minerva__tab-container {
	display: none;
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.page-actions-menu {
	display: none;
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#content {
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}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
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.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
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#footer-places {
  margin-bottom: 15px;
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#footer-places a:link {
  color: #CCCCCC;
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#footer-places a:visited {
  color: #AAAAAA;
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#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}</text>
    <sha1>bca7198f008cba76bd99829e65f645c05a1e0876</sha1>
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  <revision>
    <id>46</id>
    <parentid>45</parentid>
    <timestamp>2023-10-26T06:42:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Add some padding before page headings</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="949" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
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.minerva__tab-container {
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.page-actions-menu {
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#content {
	border-top: 2px solid #990000;
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.minerva-footer {
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.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
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.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
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#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
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#footer-places a:visited {
  color: #AAAAAA;
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#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}</text>
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    <timestamp>2023-10-26T10:53:35Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Place refbase logo before refbase badge</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="1061" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
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h1 { 
	text-align: center;
	padding-top: 15px;
	color: #990000;
}

.mw-headline { 
	color: #990000;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
}

.minerva-footer {
	color: #F0F0F0;
	background-color: #073970;
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.footer-content:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon.svg');
}

.last-modified-bar {
	border-bottom: 3px solid #990000;
	background-color: #EAECF0;
}

#footer-places {
  margin-bottom: 15px;
}

#footer-places a:link {
  color: #CCCCCC;
}

#footer-places a:visited {
  color: #AAAAAA;
}

#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}

#refbase-badge:before{
	content: url('https://wiki.refbase.net/skins/common/images/refbase_icon_large.png');
}</text>
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    <timestamp>2023-10-26T11:11:00Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Properly position refbase logo to the left of the refbase badge</comment>
    <model>css</model>
    <format>text/css</format>
    <text bytes="1105" xml:space="preserve">/* CSS placed here will be applied to all skins */

.branding-box {
  font-weight: bold;
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h1 { 
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	padding-top: 15px;
	color: #990000;
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.mw-headline { 
	color: #990000;
}

.minerva__tab-container {
	display: none;
}

.page-actions-menu {
	display: none;
}

#content {
	border-top: 2px solid #990000;
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.footer-content:before{
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#footer-places a:visited {
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#refbase-badge {
	font-weight: normal;
	font-family: luxi serif, georgia, times new roman, times, serif;
	font-size: 220%;
	color: #990000;
	background: none;
}

html&gt;body #refbase-badge {
	/* hidden from IE */
	margin: -8pt;
}

#refbase-badge:before{
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	position: absolute;
	top: -36px;
	left: 0;
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</page>
<page arvcontinue="">
  <title>refbase:Community portal</title>
  <ns>4</ns>
  <id>10</id>
  <revision>
    <id>11</id>
    <timestamp>2023-10-24T12:54:24Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 03-Nov-2008 (original wiki page: refbase:Community_Portal)</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1551" xml:space="preserve">We like to hear from you!

== Help ==

If you've got questions or encounter any problems using refbase you're welcome to use our [http://sourceforge.net/forum/forum.php?forum_id=218758 help forum] or submit your feedback to our [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Discuss ==

If you need assistance from other users, want to share tips or discuss existing or potential features you're welcome to browse, search or post to our [http://sourceforge.net/forum/forum.php?forum_id=218757 discussion forum] or the [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Feature Requests ==

If you've got some suggestions how refbase can be improved you're welcome to share your ideas [[feature request|here]]. Alternatively, you can use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum] to request or discuss any new features. You may be also interested in our list of [[Planned_feature_additions|planned features]].

== Get Involved ==

If you'd like to contribute to the ongoing development of refbase please send us an [[Special:Emailuser/WikiSysop|email]]. For bugs or feature requests please use our [http://sourceforge.net/forum/?group_id=64647 forums] or [http://sourceforge.net/mail/?group_id=64647 mailinglists]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

You can also [[Special:Emailuser/WikiSysop|contact us directly via email]].
__NOTOC__</text>
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  </revision>
  <revision>
    <id>12</id>
    <parentid>11</parentid>
    <timestamp>2023-10-24T12:56:21Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1569" xml:space="preserve">We like to hear from you!

== Help ==

If you've got questions or encounter any problems using refbase you're welcome to use our [http://sourceforge.net/forum/forum.php?forum_id=218758 help forum] or submit your feedback to our [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Discuss ==

If you need assistance from other users, want to share tips or discuss existing or potential features you're welcome to browse, search or post to our [http://sourceforge.net/forum/forum.php?forum_id=218757 discussion forum] or the [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Feature Requests ==

If you've got some suggestions how refbase can be improved you're welcome to share your ideas [[feature request|here]]. Alternatively, you can use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum] to request or discuss any new features. You may be also interested in our list of [[Planned_feature_additions|planned features]].

== Get Involved ==

If you'd like to contribute to the ongoing development of refbase please send us an [[Special:Emailuser/WikiSysop|email]]. For bugs or feature requests please use our [http://sourceforge.net/forum/?group_id=64647 forums] or [http://sourceforge.net/mail/?group_id=64647 mailinglists]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

You can also [[Special:Emailuser/WikiSysop|contact us directly via email]].
__NOTOC__
__NOEDITSECTION__</text>
    <sha1>32151e7a98b7274eee71d8db0000149021ea9090</sha1>
  </revision>
  <revision>
    <id>17</id>
    <parentid>12</parentid>
    <timestamp>2023-10-24T13:11:58Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update SourceForge forum links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1563" xml:space="preserve">We like to hear from you!

== Help ==

If you've got questions or encounter any problems using refbase you're welcome to use our [https://sourceforge.net/p/refbase/discussion/218758/ help forum] or submit your feedback to our [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Discuss ==

If you need assistance from other users, want to share tips or discuss existing or potential features you're welcome to browse, search or post to our [https://sourceforge.net/p/refbase/discussion/218757/ discussion forum] or the [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Feature Requests ==

If you've got some suggestions how refbase can be improved you're welcome to share your ideas [[feature request|here]]. Alternatively, you can use our [https://sourceforge.net/p/refbase/discussion/351913/ Feature Requests forum] to request or discuss any new features. You may be also interested in our list of [[Planned_feature_additions|planned features]].

== Get Involved ==

If you'd like to contribute to the ongoing development of refbase please send us an [[Special:Emailuser/WikiSysop|email]]. For bugs or feature requests please use our [https://sourceforge.net/p/refbase/discussion/ forums] or [https://sourceforge.net/p/refbase/mailman/ mailinglists]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

You can also [[Special:Emailuser/WikiSysop|contact us directly via email]].
__NOTOC__
__NOEDITSECTION__</text>
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  </revision>
</page>
<page arvcontinue="">
  <title>refbase:About</title>
  <ns>4</ns>
  <id>11</id>
  <revision>
    <id>14</id>
    <timestamp>2023-10-24T13:00:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 03-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="768" xml:space="preserve">This wiki is a community effort to document the [http://refbase.sourceforge.net/ refbase] web application.

== About refbase ==

[http://refbase.sourceforge.net/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

To learn more about refbase, please see the [[Feature_highlights|Features]] and [[Documentation]] sections in this wiki, or have a look at the [http://en.wikipedia.org/wiki/Refbase Wikipedia entry] for refbase.</text>
    <sha1>366729e50f0a93d5a4de35f25c9a72046bc2d163</sha1>
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  <revision>
    <id>15</id>
    <parentid>14</parentid>
    <timestamp>2023-10-24T13:00:46Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="787" xml:space="preserve">This wiki is a community effort to document the [http://refbase.sourceforge.net/ refbase] web application.

== About refbase ==

[http://refbase.sourceforge.net/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

To learn more about refbase, please see the [[Feature_highlights|Features]] and [[Documentation]] sections in this wiki, or have a look at the [http://en.wikipedia.org/wiki/Refbase Wikipedia entry] for refbase.

__NOEDITSECTION__</text>
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  <revision>
    <id>16</id>
    <parentid>15</parentid>
    <timestamp>2023-10-24T13:02:33Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Link to SourceForge project page</comment>
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    <format>text/x-wiki</format>
    <text bytes="886" xml:space="preserve">This wiki is a community effort to document the [https://sourceforge.net/projects/refbase/ refbase] web application.

== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists. You can have a look at a [[more detailed introduction]] to the aims and history of refbase.

To learn more about refbase, please see the [[Feature_highlights|Features]] and [[Documentation]] sections in this wiki, visit its [https://sourceforge.net/projects/refbase/ SourceForge project page] or have a look at the [http://en.wikipedia.org/wiki/Refbase Wikipedia entry] for refbase.

__NOEDITSECTION__</text>
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</page>
<page arvcontinue="">
  <title>MediaWiki:Sidebar</title>
  <ns>8</ns>
  <id>12</id>
  <revision>
    <id>20</id>
    <timestamp>2023-10-24T14:05:29Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Don't display randompage in sidebar navigation</comment>
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    <text bytes="177" xml:space="preserve">
* navigation
** mainpage|mainpage-description
** recentchanges-url|recentchanges
&lt;!-- ** randompage-url|randompage --&gt;
** helppage|help-mediawiki
* SEARCH
* TOOLBOX
* LANGUAGES</text>
    <sha1>b25743ea59d5ca51ebae8dda5bb0940e993a1e44</sha1>
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</page>
<page arvcontinue="">
  <title>Main features</title>
  <ns>0</ns>
  <id>13</id>
  <revision>
    <id>30</id>
    <timestamp>2023-10-25T08:37:32Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 23-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9460" xml:space="preserve">== General features ==

The refbase web site lists [[Feature highlights|feature highlights]] (including screenshots) of the current release version. Main features include:

* a clean and standardized interface that attempts to be as web standards compliant as possible
* a multitude of [[Searching|search options]], including quick, simple, advanced as well as powerful SQL search options
* various display options: 
** list view: offers customizable and sortable columns
** details view: shows all fields of a particular record
** cite view: displays record entries in a citation style chosen by the user
** print view: eases printing or copying of records
* search within results functionality which provides an easy way of refining your search query
* user-specific fields for personal keywords, notes, etc
* save any search query together with the current display settings
* automatic email announcements for newly added records
* dynamic [[RSS_features|RSS feeds]] for recently added/edited records as well as for any custom user query
* export records to MODS XML, Endnote, RIS or BibTeX (via bibutils)
* link records to other records in the database (using static or dynamic links)
* extract literature cited within a text and build an appropriate reference list

If you've got some suggestions how refbase can be improved you're welcome to share your ideas [[feature request|here]]. Alternatively, you can use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests] forum or the [https://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk] mailing list to request or discuss any new features.

== refbase-0.9.5 ==

A short overview of the major feature additions in refbase-0.9.5 is given below. Please see the [[Release_notes#refbase-0.9.5|refbase-0.9.5 release notes]] for a more detailed list of the major feature additions, changes and bug fixes since refbase-0.9.0.

=== Feature additions ===

* Added support for '''new resource types''': Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software.

* refbase can now '''import''' from '''SciFinder''' and '''Endnote XML'''.

* refbase now supports direct '''import''' from arXiv.org &amp; CrossRef.org: enter one or more '''arXiv IDs''', '''DOIs''' or '''OpenURLs''', and refbase will fetch &amp; import the corresponding record metadata.

* refbase now allows to '''export''' references as '''Atom XML''', '''Simple Dublin Core XML''', '''Word 2007 XML Bibliography''' or in the '''ADS''' and '''ISI Web of Science''' tagged formats.

* refbase can now '''output citations''' in '''AMA''', '''APA''', '''Chicago''', '''Harvard''', '''MLA''', or '''Vancouver''' citation style as well as in '''LaTeX bibliography''' (.bbl) format.

* refbase sports a '''refined interface''': 
** Redesigned the main page, page footer &amp; header as well as the forms on the results pages.
** The '''Quick Search''' form is now always '''available in''' the '''page header'''.
** refbase now generates '''auto-completions''' (or '''search suggestions''') for text entered by the user in text entry fields of the refbase interface.
** '''Forms''' on search results pages '''can''' now '''be hidden'''.
** Search results can be browsed &amp; searched in '''three different views''': List view, Citations, and Details.
** '''Additional record info''' (keywords, abstract, etc) and links to cite/export the record can now be displayed '''underneath each citation'''.

* refbase now supports [[OpenSearch service|'''OpenSearch''']] which allows clients to search refbase and retrieve results in a standardized manner. As an example, this enables Firefox &amp; IE users to '''search refbase directly from their browser's toolbar'''.

* For the current session, refbase now offers a '''query history''' with links to any previous search results.

* refbase offers initial support to '''search &amp; manage duplicates'''.

* Added support for direct upload of references from '''[http://www.sonnysoftware.com/ Bookends]'''.

* The refbase ''show.php'' API now allows to [[Integrating_refbase_into_your_web_site|'''dynamically include results''']] from a refbase server '''into other web pages'''.

* Added a "main fields" search option to the "Quick Search" form which allows to '''search all of the main fields at once'''. The list of "main fields" can be specified individually for each user.

* The default number of records per page can now be specified individually for each user.

* The [[Command_line_clients|''''refbase' command line client''']] now allows to  '''append found records''' to a local BibTeX or MODS/SRW XML file (if they don't yet exist in that file), and '''update existing records''' in that file if their modification date on the server is more recent.

* The [[Command_line_clients|''''refbase' command line client''']] can now '''extract citation IDs''' from a file and '''retrieve matching records''' from a refbase database. Supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, and (MODS|SRW|Endnote) .xml

== refbase-0.9.0 ==

refbase-0.9.0 features many enhancements and bug fixes. Major additions and fixes are listed below:

=== Feature additions ===

* refbase now offers web-based '''batch import''' capabilities for records from various common bibliographic formats (Endnote, RIS, BibTeX, MODS XML) and online databases (PubMed, ISI Web of Science, Cambridge Scientific Abstracts, COPAC).

* refbase offers '''import''' from PubMed.gov '''via PubMed ID''', i.e., you can simply enter one or more PMID identifiers and refbase will fetch and import all corresponding source data.

* refbase can now '''export''' selected references '''to OpenDocument spreadsheet format''' ("ODF XML"). You can specify this ODS file as a bibliographic database in OO.o which allows you to easily [[OO.o Writer integration|integrate a refbase database with OpenOffice.org Writer]].

* refbase can now '''output citations as RTF, PDF, LaTeX''' or structured/plain text.

* Added support for the '''SRU''' (Search/Retrieve via URL) standard search protocol for Internet search queries. This provides a '''webservice''' that allows clients to access a refbase database using a standard query syntax (CQL) and retrieve results in structured format (MODS XML wrapped into SRW XML). ([[Search/Retrieve_web_services|more info]])

* refbase now comes with two '''[[command line clients]]''' written in Perl which allow you to:
** search a refbase online database from the command line and retrieve results in various formats
** upload data in various formats to a refbase online database from the command line

* Added new sort orders that '''output citations sorted by resource type''' (peer-reviewed publications, monographs, book contributions, theses, etc).

* refbase now automatically generates links to '''OpenURL and ISBN resolvers'''. An OpenURL resolver can redirect users to the "most appropriate" (full-text) copy of a work to which a user has a valid subscription. ([[Standard link resolver support: OpenURL &amp; COinS|more info]])

* For each displayed record, refbase now '''embeds bibliographic metadata''' within its HTML pages according to the '''COinS (ContextObjects in Spans)''' specification. This allows third-party tools (such as web browser extensions) to automatically discover and link to records or extract the embedded metadata into bibliographic search or storage systems. ([[Standard link resolver support: OpenURL &amp; COinS|more info]])

* The main page as well as the header &amp; footer feature "'''Show all'''" '''links''' which will display all records in the database.

* In Details view, refbase now prints an URL that directly links to the given record ("'''Permanent link to this record'''").

* Search forms offer two new drop-down items ("'''is within range'''" and "'''is within list'''") for numeric fields. Examples:

{| border="0" cellpadding="6" style="background:#F9F9F9; border:dashed 1px #3A70A9"
|- align="left"
! Select !! Enter !! Finds
|-
| is within range || 10-20 || 10, 11, 12, ..., 18, 19, 20
|-
| is within list || 10 20 30 || 10, 20, 30
|}

* The admin can now control which links shall be displayed in List view and Citation view. By this, it's now easy to provide PDF '''download links in Citation view'''.

* Upon file upload, '''file and sub-directory names''' can now be '''auto-generated''' according to a flexible [[Placeholder_syntax|naming scheme]]. This allows, for example, to automatically file uploaded PDFs first by first author and then by year, and rename the files according to their bibliographic information.

* It's now possible to perform '''case transformations''' on generated file and directory names before filing.

* '''Cite keys''' can now be '''auto-generated''' on export and users can specify their own cite key patterns (using the same [[Placeholder_syntax|placeholder system]] that's used for auto-generation of file/dir names and ISBN links).

* The formatting of '''Text Citations''' can now be controlled individually for each user. The same placeholders as with file/dir names, cite keys, etc are supported.

=== Bug fixes ===

* A user is only allowed to search for files (via Advanced Search or SQL Search) if he has permission to view/download files. The contents of the file field will be also hidden from the user in edit mode if necessary.

* The user-specific language setting is now honoured correctly.


[[Category:General]]</text>
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    <id>31</id>
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    <contributor>
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    <model>wikitext</model>
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    <text bytes="9478" xml:space="preserve">== General features ==

The refbase web site lists [[Feature highlights|feature highlights]] (including screenshots) of the current release version. Main features include:

* a clean and standardized interface that attempts to be as web standards compliant as possible
* a multitude of [[Searching|search options]], including quick, simple, advanced as well as powerful SQL search options
* various display options: 
** list view: offers customizable and sortable columns
** details view: shows all fields of a particular record
** cite view: displays record entries in a citation style chosen by the user
** print view: eases printing or copying of records
* search within results functionality which provides an easy way of refining your search query
* user-specific fields for personal keywords, notes, etc
* save any search query together with the current display settings
* automatic email announcements for newly added records
* dynamic [[RSS_features|RSS feeds]] for recently added/edited records as well as for any custom user query
* export records to MODS XML, Endnote, RIS or BibTeX (via bibutils)
* link records to other records in the database (using static or dynamic links)
* extract literature cited within a text and build an appropriate reference list

If you've got some suggestions how refbase can be improved you're welcome to share your ideas [[feature request|here]]. Alternatively, you can use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests] forum or the [https://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk] mailing list to request or discuss any new features.

== refbase-0.9.5 ==

A short overview of the major feature additions in refbase-0.9.5 is given below. Please see the [[Release_notes#refbase-0.9.5|refbase-0.9.5 release notes]] for a more detailed list of the major feature additions, changes and bug fixes since refbase-0.9.0.

=== Feature additions ===

* Added support for '''new resource types''': Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software.

* refbase can now '''import''' from '''SciFinder''' and '''Endnote XML'''.

* refbase now supports direct '''import''' from arXiv.org &amp; CrossRef.org: enter one or more '''arXiv IDs''', '''DOIs''' or '''OpenURLs''', and refbase will fetch &amp; import the corresponding record metadata.

* refbase now allows to '''export''' references as '''Atom XML''', '''Simple Dublin Core XML''', '''Word 2007 XML Bibliography''' or in the '''ADS''' and '''ISI Web of Science''' tagged formats.

* refbase can now '''output citations''' in '''AMA''', '''APA''', '''Chicago''', '''Harvard''', '''MLA''', or '''Vancouver''' citation style as well as in '''LaTeX bibliography''' (.bbl) format.

* refbase sports a '''refined interface''': 
** Redesigned the main page, page footer &amp; header as well as the forms on the results pages.
** The '''Quick Search''' form is now always '''available in''' the '''page header'''.
** refbase now generates '''auto-completions''' (or '''search suggestions''') for text entered by the user in text entry fields of the refbase interface.
** '''Forms''' on search results pages '''can''' now '''be hidden'''.
** Search results can be browsed &amp; searched in '''three different views''': List view, Citations, and Details.
** '''Additional record info''' (keywords, abstract, etc) and links to cite/export the record can now be displayed '''underneath each citation'''.

* refbase now supports [[OpenSearch service|'''OpenSearch''']] which allows clients to search refbase and retrieve results in a standardized manner. As an example, this enables Firefox &amp; IE users to '''search refbase directly from their browser's toolbar'''.

* For the current session, refbase now offers a '''query history''' with links to any previous search results.

* refbase offers initial support to '''search &amp; manage duplicates'''.

* Added support for direct upload of references from '''[http://www.sonnysoftware.com/ Bookends]'''.

* The refbase ''show.php'' API now allows to [[Integrating_refbase_into_your_web_site|'''dynamically include results''']] from a refbase server '''into other web pages'''.

* Added a "main fields" search option to the "Quick Search" form which allows to '''search all of the main fields at once'''. The list of "main fields" can be specified individually for each user.

* The default number of records per page can now be specified individually for each user.

* The [[Command_line_clients|''''refbase' command line client''']] now allows to  '''append found records''' to a local BibTeX or MODS/SRW XML file (if they don't yet exist in that file), and '''update existing records''' in that file if their modification date on the server is more recent.

* The [[Command_line_clients|''''refbase' command line client''']] can now '''extract citation IDs''' from a file and '''retrieve matching records''' from a refbase database. Supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, and (MODS|SRW|Endnote) .xml

== refbase-0.9.0 ==

refbase-0.9.0 features many enhancements and bug fixes. Major additions and fixes are listed below:

=== Feature additions ===

* refbase now offers web-based '''batch import''' capabilities for records from various common bibliographic formats (Endnote, RIS, BibTeX, MODS XML) and online databases (PubMed, ISI Web of Science, Cambridge Scientific Abstracts, COPAC).

* refbase offers '''import''' from PubMed.gov '''via PubMed ID''', i.e., you can simply enter one or more PMID identifiers and refbase will fetch and import all corresponding source data.

* refbase can now '''export''' selected references '''to OpenDocument spreadsheet format''' ("ODF XML"). You can specify this ODS file as a bibliographic database in OO.o which allows you to easily [[OO.o Writer integration|integrate a refbase database with OpenOffice.org Writer]].

* refbase can now '''output citations as RTF, PDF, LaTeX''' or structured/plain text.

* Added support for the '''SRU''' (Search/Retrieve via URL) standard search protocol for Internet search queries. This provides a '''webservice''' that allows clients to access a refbase database using a standard query syntax (CQL) and retrieve results in structured format (MODS XML wrapped into SRW XML). ([[Search/Retrieve_web_services|more info]])

* refbase now comes with two '''[[command line clients]]''' written in Perl which allow you to:
** search a refbase online database from the command line and retrieve results in various formats
** upload data in various formats to a refbase online database from the command line

* Added new sort orders that '''output citations sorted by resource type''' (peer-reviewed publications, monographs, book contributions, theses, etc).

* refbase now automatically generates links to '''OpenURL and ISBN resolvers'''. An OpenURL resolver can redirect users to the "most appropriate" (full-text) copy of a work to which a user has a valid subscription. ([[Standard link resolver support: OpenURL &amp; COinS|more info]])

* For each displayed record, refbase now '''embeds bibliographic metadata''' within its HTML pages according to the '''COinS (ContextObjects in Spans)''' specification. This allows third-party tools (such as web browser extensions) to automatically discover and link to records or extract the embedded metadata into bibliographic search or storage systems. ([[Standard link resolver support: OpenURL &amp; COinS|more info]])

* The main page as well as the header &amp; footer feature "'''Show all'''" '''links''' which will display all records in the database.

* In Details view, refbase now prints an URL that directly links to the given record ("'''Permanent link to this record'''").

* Search forms offer two new drop-down items ("'''is within range'''" and "'''is within list'''") for numeric fields. Examples:

{| border="0" cellpadding="6" style="background:#F9F9F9; border:dashed 1px #3A70A9"
|- align="left"
! Select !! Enter !! Finds
|-
| is within range || 10-20 || 10, 11, 12, ..., 18, 19, 20
|-
| is within list || 10 20 30 || 10, 20, 30
|}

* The admin can now control which links shall be displayed in List view and Citation view. By this, it's now easy to provide PDF '''download links in Citation view'''.

* Upon file upload, '''file and sub-directory names''' can now be '''auto-generated''' according to a flexible [[Placeholder_syntax|naming scheme]]. This allows, for example, to automatically file uploaded PDFs first by first author and then by year, and rename the files according to their bibliographic information.

* It's now possible to perform '''case transformations''' on generated file and directory names before filing.

* '''Cite keys''' can now be '''auto-generated''' on export and users can specify their own cite key patterns (using the same [[Placeholder_syntax|placeholder system]] that's used for auto-generation of file/dir names and ISBN links).

* The formatting of '''Text Citations''' can now be controlled individually for each user. The same placeholders as with file/dir names, cite keys, etc are supported.

=== Bug fixes ===

* A user is only allowed to search for files (via Advanced Search or SQL Search) if he has permission to view/download files. The contents of the file field will be also hidden from the user in edit mode if necessary.

* The user-specific language setting is now honoured correctly.


[[Category:General]]
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</page>
<page arvcontinue="">
  <title>Planned feature additions</title>
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  <revision>
    <id>32</id>
    <timestamp>2023-10-25T08:41:54Z</timestamp>
    <contributor>
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    <comment>Original page content from 22-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="24536" xml:space="preserve">This page lists planned feature additions:

'''Important''': Please note that the items listed below are simply suggestions for improving refbase and that we cannot (and don't want to) speculate on whether or when any of the listed features will be added to refbase.

== General ==

=== Resource types ===

Goal: Increase number of supported resource types.

Priority: 6

Status: added types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Report, Patent, Software

Progress: 50%

Description: refbase should allow users to choose from a variety of additional resource types including conference proceeding, patent, report, newspaper article, computer program, etc. All these types should invoke appropriate output on citation. In addition, the admin should be allowed to add additional resource types and users should be able to disable any unused types.

=== Migrate to more common libraries ===

Goal: To work under a larger number of configurations &amp; to depend on only well-maintained code.

Priority: 3

Status: not started

Progress: 0%

Description: We should consider migrating away from the ActiveLink XML library, as it isn't maintained. refbase should also be able to use MySQLi.

== Installation and updates ==

=== Redirect from ''index.php'' to ''install.php'' or ''update.php'' ===

Goal: refbase should direct to ''install.php'' or ''update.php'' as needed.

Priority: 6

Status: not started

Progress: 0%

Description: If the database doesn't exist, refbase should direct to ''install.php''. A version number or date for refbase could be stored in the database. If it is older than a version variable in ''index.php'', ''index.php'' could redirect to the update script.

=== Improvements to ''install.php'' ===

Goal: The ''install.php'' script should verify required server settings and provide more options for installation on different server setups.

Priority: 6

Status: not started

Progress: 0%

Description: 1) ''install.php'' should check required server settings prior to installation, and report possible problems in advance. 2) ''install.php'' should allow for installation into an existing database by providing an option for a table prefix that will be used for the refbase MySQL tables (currently, this can only be done by editing some configuration files). 3) To allow for web-based installation on shared hosts, ''install.php'' could offer an option to use an existing MySQL user (instead of setting up its own MySQL user which requires a MySQL admin user &amp; password). 4) ''install.php'' should provide an option to omit the sample data, i.e. install with a blank database.

=== Allow editing of configuration scripts through a web interface ===

Goal: Offer a web interface to the settings provided in ''ini.inc.php'', ''db.inc.php' and other config files.

Priority: 3

Status: not started

Progress: 0%

Description: Upon installation or update, refbase could list the settings in the various configuration files that are now manually edited &amp; allow users to make changes with the web interface.

== Searching ==

=== Search for duplicates ===

Goal: Offer the user means for handling duplicate database entries.

Priority: 4

Status: in development

Progress: 40%

Description: The database should offer means to easily spot duplicate entries and mark particular records as original (or duplicate) entry. Search features should allow users to exclude duplicate entries from the results list. It would be preferable if a smart dup detection mechanism such as phonetic matching could be used. See the [http://dev.mysql.com/doc/refman/4.1/en/string-functions.html MySQL string functions] &lt;code&gt;SOUNDEX&lt;/code&gt; and &lt;code&gt;SOUNDS LIKE&lt;/code&gt;.

=== ''OR'' search capabilities ===

Goal: Allow ''OR'' searches via the GUI.

Priority: 3

Status: not started

Progress: 0%

Description: When searching via one of the dedicated search pages, users should be able to specify whether a search on multiple fields will invoke an ''AND'' or an ''OR'' query (currently, entering search terms in multiple fields will always connect search terms with ''AND''). In addition, the "Search within Results" query form should allow users to expand the current result set, i.e. add found results to the existing list of results.

=== Simple handling of accented characters or umlauts ===

Goal: Allow naive users to search for accented characters by using the unaccented character and vice-versa.

Priority: 3

Status: not started

Progress: 0%

Description: If a search query contains no accents, it might be desirable to automatically search for commonly accented characters (especially in the Quick and Simple searches). If a user enters 'Jon', refbase could search for 'J[oÛˆ¯]n'. Similarly, it might be desirable to search for unaccented characters if a query contains an accent. If a user entered in 'JÛn', refbase might search instead for 'J[oÛ]n'. Naturally, there should be a mechanism for "advanced users" to have exact searches (perhaps by requiring a pre or post fix for more precise handling of (un)accented search strings.

=== Cross-site searches ===

Goal: Allow users to search and display results from other databases.

Priority: 2

Status: not started

Progress: 0%

Description: refbase should allow for cross-site searches both through other installations of refbase as well as through other bibliographic databases of the [http://bibliophile.sourceforge.net/ Bibliophile initiative]. Support for web service protocols such as [[Search/Retrieve_web_services|SRU]] and [[#OpenSearch support|OpenSearch]] will ease communication between different applications.

== Adding/Editing of records ==

=== Import ===

Goal: Offer direct data import from MODS XML.

Priority: 6

Status: not started

Progress: 0%

Description: refbase currently offers a number of native import scripts, as well as scripts which use [[Bibutils]] to convert formats to something which refbase can read. Long-term plans are to provide native import capabilities for [http://www.loc.gov/standards/mods/ MODS XML]. [[Importing records]] describes the import functionality available in refbase and future plans on import.

=== Direct import via arXiv ID ===

Goal: Use arXiv API to directly fetch and import records &amp; PDFs from arXiv.org.

Priority: 5

Status: import from arXiv.org has been fully implemented, though some aspects (such as parsing of the "Journal Ref" string) might need some further testing and fine-tuning

Progress: 95%

Description: refbase allows to directly fetch and import records from [http://www.pubmed.gov PubMed.gov] via their PubMed ID. A similar feature should be added for the [http://www.arxiv.org/ arXiv.org] e-Print archive. The [http://export.arxiv.org/api_help/docs/user-manual.html arXiv API] allows for HTTP GET queries by arXiv ID and returns OpenSearch Atom feeds with basic metadata (title, author(s), publication date, abstract, and journal info if given) and any URLs (HTML, PDF, DOI) associated with an article. refbase should parse the OpenSearch response and add new database records for each feed entry. Ideally, associated PDFs would be fetched as well and stored with the record.

=== Record-type specific forms ===

Goal: Simplify manual data input by providing record-type specific forms.

Priority: 2

Status: not started

Progress: 0%

Description: Record-type specific forms would guide a user by only showing those fields that are required for a particular record-type (like journal articles, book chapters or whole books). Record-type specific forms might not be necessary if the current "Add/Edit Record" form would be able to dynamically indicate required fields for a given record-type.

=== Input validation ===

Goal: refbase should dynamically validate input in the "Add/Edit Record" form.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should provide on-the-fly validation of data while a user inputs or edits data in the "Add/Edit Record" form. This would help users to ensure correct formatting for fields that require a specific string formatting (such as the ''author'' field). Dynamic form input validation may be best realized using [http://en.wikipedia.org/wiki/AJAX AJAX] style methods.

=== Auto-filling of fields ===

Goal: refbase should auto-fill fields if possible.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should be able to auto-fill empty fields based on information available in other fields and/or tables. This is especially useful if a flat database design is maintained. A typical application would be the auto-filling of journal-related fields (e.g. ''publisher'', ''place'', ''abbrev_journal'', ''language'' or ''summary_language'') from a journal database if the journal name (or ISSN) can be uniquely matched. If no journal info is available in the refbase journal database, a public service such as http://journalseek.net/ could be used for information retrieval and the fetched journal data could be automatically added to refbase's own journal database. Similarly, refbase could use web services from CrossRef (see [http://hublog.hubmed.org/archives/001624.html HubLog post] and links therein), WorldCat ([http://xissn.worldcat.org/xissnadmin/index.htm xISSN] &amp; [http://www.worldcat.org/affiliate/webservices/xisbn/app.jsp xISBN]) or LibraryThing ([http://www.librarything.com/thingology/2006/06/introducing-thingisbn_14.php thingISBN]) to supplement record metadata.

=== Auto-completion of field input ===

Goal: refbase should auto-complete user input in the "Add/Edit Record" form.

Priority: 4

Status: auto-completion has been fully implemented for the "Add/Edit Record" form and search suggestions are provided in some of the search forms (but they're not yet available in the "Advanced Search" and "Library Search" forms)

Progress: 95%

Description: It would be helpful if refbase would offer auto-completion features for fields of the "Add/Edit Record" form. This would allow users to start typing a string, then choose from a list of matching values (such as authors, keywords or journal names) that already exist in the database. Ideally, such a feature would not interfere with browser-specific auto-completion features and would be platform/browser agnostic. One way of implementing this would be a pop-up window where a generic database value browser would be combined with "Search within Results" functionality, and selected values would be written/appended to the field that's currently selected in the "Add/Edit Record" form.

=== Multiple files per record ===

Goal: refbase should allow users to upload multiple files per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to upload one file per record. It would be useful if multiple files could be attached to a given record. This would allow users to upload different representations, variants or versions of the same publication. Besides the final PDF, users could then attach a Powerpoint presentation or an audio file of an associated talk (though, in a strictly hierarchical design, talks or posters may warrant different but related records). Other use cases could be the upload of supplementary material or different manuscript revisions during collaborative preparation of an article, or the upload of a publicly available Open Access version (such as preprints or postprints). Upon upload, users should be able to specify file info (such as file type, language or a description) and access permissions individually for each file.

=== Multiple URLs per record ===

Goal: refbase should allow users to specify multiple URLs per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to specify one URL per record. It would be useful if multiple URLs could be added to a given record. While the primary URL could point to the publication's entry at the publisher site, additional URLs could point to, say, further info/news about the publication, any supplementary material, or related discussion located elsewhere. As is true for multiple files, some options to categorize and/or describe the given URLs as well as individual access permissions might be useful.

=== Support foreign record identifiers ===

Goal: refbase should support record identifiers from foreign repositories (e.g. from [http://www.pubmed.gov PubMed.gov] or [http://www.arxiv.org/ arXiv.org]) explicitly, and auto-generate links back to these repositories.

Priority: 5

Status: not started

Progress: 0%

Description: Upon import, refbase currently puts foreign record identifiers (such as IDs from arXiv, ISI Web of Science, PubMed, or SciFinder) into the ''notes'' field. It would be nice, however, if these record identifiers would be stored in some dedicated field(s). This would allow refbase to auto-generate links back to the corresponding record entries at the foreign repositories.

== Sharing ==

=== Public groups (tags) ===

Goal: Allow users to collectively share and categorize groups of records.

Priority: 6

Status: not started

Progress: 0%

Description: We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system.

=== User comments ===

Goal: Allow users to comment on particular records and exchange their thoughts with others.

Priority: 3

Status: not started

Progress: 0%

Description: We imagine a comment system where multiple comments would be allowed for a particular record and where comments could be made public, group-specific or private. Comments could be searched and displayed similar to (and in combination with) bibliographic references. Here's an ASCII mockup of how we envision such a system:

 +-------------------------------------------------------------------+
 |                                                                   |
 |  Cota GF, Horne EPW (1989) Physical control of Arctic ice algal   |
 |  production. Mar Ecol Prog Ser 52(2):111-121                      |
 |                                                                   |
 |  Matthias Steffens  |  This is an essential article that provides |
 |  *****              |  a good dataset on environmental control of |
 |  2005-04-27 23:33   |  primary production in polar areas.         |
 |                                                                   |
 +-------------------------------------------------------------------+
 |                                                                   |
 |  Mock T (2002) In situ primary production in young Antarctic sea  |
 |  ice. Hydrobiologia 470(1-3):127-132                              |
 |                                                                   |
 |  Matthias Steffens  |  Given the inaccessibility of the location  |
 |  ***                |  it's valuable data nonetheless. In situ    |
 |  2004-12-18 16:05   |  measurements are still very rare.          |
 |                                                                   |
 |  Paul Miller        |  I didn't get the point of this article.    |
 |  *                  |  IMHO, it's based on a weak dataset and     |
 |  2004-12-03 12:19   |  the conclusions are fuzzy.                 |
 |                                                                   |
 |  Matthias Steffens  |  Did anybody read this one? I'd appreciate  |
 |                     |  your opinions on the used method and       |
 |  2004-12-01 11:22   |  how this relates to existing methods.      |
 |                                                                   |
 +-------------------------------------------------------------------+

According to the above visualization, comments would print below the reference they are referring to. The reference would be displayed as a citation. Multiple citations with multiple comments could be displayed and you could search within results as usual. Note the stars which indicate the users rating. Users could edit/delete their own comments and decide who'll be able to see them (everyone, certain group(s) or private).

=== Better integration with desktop reference managers ===

Goal: Provide means for easy download of records to desktop reference managers, and for direct record upload to a refbase database.

Priority: 5

Status: for [http://www.sonnysoftware.com/ Bookends], "Upload to refbase" functionality has been added

Progress: 5%

Description: refbase should integrate with desktop reference managers (such as [http://bibdesk.sourceforge.net/ BibDesk], [http://www.sonnysoftware.com/ Bookends], [http://jabref.sourceforge.net/ JabRef], [http://mekentosj.com/papers/ Papers] or [http://www.zotero.org/ Zotero]) so that records stored in a refbase database can be easily retrieved from within these applications. Zotero can already extract bibliographic metadata from refbase's web pages via [[COinS]] or [[unAPI service|unAPI]], and something similar could work for other apps that feature web views. In addition, it would be desirable if users could search an online refbase database from within their desktop reference managers. The refbase search &amp; retrieve webservices offer standardized APIs for this, such as the [[Search/Retrieve_web_services|SRU/W webservice]] or [[#OpenSearch support|OpenSearch]] in conjunction with the existing [[unAPI service]]. Finally, it would be also useful if users of desktop reference managers could upload (and eventually synch) records to a refbase server directly from within their desktop application. In case of Zotero, "upload to refbase" functionality could be developed via an [http://dev.zotero.org/docs/sample_utility Zotero utility].

== Webservices ==

=== OpenSearch support ===

Goal: Allow OpenSearch clients to query refbase and return found results in OpenSearch response format.

Priority: 6

Status: OpenSearch support has been implemented with support for auto-discovery, multiple response formats (HTML, Atom, RSS, SRW_DC XML, SRW_MODS XML), simple CQL searches and support for search suggestions (returned in JSON or HTML); a better CQL parser would be desirable

Progress: 95%

Description: Similar to the refbase [[Search/Retrieve_web_services|SRU/W webservice]], refbase should support an [[OpenSearch service|OpenSearch]] webservice. OpenSearch capable clients would be able to [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_Query_element query] a refbase database and retrieve search results in an OpenSearch [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_response_elements response format], e.g. RSS 2.0 or Atom 1.0, plus the OpenSearch response extensions. This would also allow to integrate several refbase servers (or other OpenSearch capable servers) via [[Planned_feature_additions#Cross-site_searches|cross-site searches]]. When implemented, refbase should support auto-discovery to allow for [http://developer.mozilla.org/en/docs/Creating_OpenSearch_plugins_for_Firefox search plugins]. Eventual support for JSON for fetching of search suggestions would be nice.

=== API ===

Goal: Provide an API that allows clients to query a refbase database, retrieve results in a structured format and modify any database information.

Priority: 5

Status: not started

Progress: 0%

Description: Opposed to pure search/retrieve webservices (such as [[Search/Retrieve_web_services|SRU/W]] and [[OpenSearch service|OpenSearch]]), a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] API should also allow clients to send requests that ''alter'' the database, i.e. add, edit or delete records, meta-data or users. This will allow for easy integration with third-party tools and enable the development of alternative interfaces to a refbase database. It would be desirable to support an existing framework such as Google's [http://code.google.com/apis/gdata/index.html GData], [http://www.ukoln.ac.uk/repositories/digirep/index/SWORD SWORD] (Simple Web-service Offering Repository Deposit), or the [http://www.loc.gov/standards/sru/record-update/ Record Update service] that is proposed by the SRU community.

=== OAI Protocol for Metadata Harvesting ===

Goal: Provide (yet another) standard way for software to retrieve information from refbase. Eventually provide a mechanism for retrieval from arxiv/dspace/eprints, and other software which is targeted at larger institutions.

Priority: 5

Status: implemented support for the simple/unqualified Dublin Core (OAI_DC) XML format which is a prerequisite for OAI-PMH

Progress: 10%

Description: [http://www.openarchives.org/OAI/openarchivesprotocol.html The Open Archives Initiative Protocol for Metadata Harvesting], which is implemented by [http://software.eprints.org/ EPrints] and [http://www.dspace.org/ DSpace] uses Dublin Core XML over HTTP. This is harvested by google and yahoo and others.

== Citation support ==

=== Increase number of available citation styles ===

Goal: Add most commonly used citation styles and generally increase the number of available styles.

Priority: 6

Status: added styles: AMA, APA, Chicago, Harvard (3 variants), MLA, Vancouver

Progress: 75%

Description: By default, refbase should include at least the most universal styles (i.e. APA, MLA, Chicago, Harvard, Turabian, CB, CGOS, CBE, AMA). Besides that, it would be nice to increase the list of available citation styles substantially.

=== User-customizable citation styles ===

Goal: Allow users to create custom citation styles, preferably via the use of a plugin structure.

Priority: 4

Status: not started

Progress: 0%

Description: Currently, citation styles are defined as PHP functions which is very powerful but not very user friendly. We plan to enhance the cite feature by adding support for other (more general) citation formats. We'd like to integrate refbase with other solutions which offer users an easier way of adding or editing any citation styles. Projects such as Mark Grimshaw's [http://sourceforge.net/project/showfiles.php?group_id=113285&amp;package_id=150961 OSBib] or [http://xbiblio.sourceforge.net/ xbiblio] developed by Bruce D'Arcus come to mind. Some implementation of CSL (backed by Bruce and used by Zotero) would be nice.

== Export ==

== Access permissions ==

=== Record-specific permissions ===

Goal: Offer fine-grained access control on record-level.

Priority: 6

Status: not started

Progress: 0%

Description: The creator (or the admin) of a record should be able to specify who will be allowed to view a particular record. For each record, an authorized user should be able to set the record visibility to everyone, private or to particular groups of database users. Separate access control settings should be provided for file downloads and edits.

== Metadata and Microformats ==

=== Embedded RDF ===

Goal: Embed citation metadata in HTML pages as machine-readable RDF which may be processed by clients.

Priority: 5

Status: not started

Progress: 0%

Description: [http://en.wikipedia.org/wiki/Resource_Description_Framework RDF] is less supported than [[COinS]], but is a useful alternative that has some advantages (such as multiple author support). This will allow client-side tools (such as [http://www.zotero.org/ Zotero]) to more easily use the data provided by refbase.

=== Other microformats? ===

Goal: Other formats may be useful as well

Priority: 1

Status: not started

Progress: 0%

Description: [http://microformats.org/wiki/citation Other citation microformats] and a [http://microformats.org/wiki/search-results-example search results microformat] might eventually be useful. It seems like COinS is the most useful at this point in time, though.

=== Wikipedia citations &amp; other UnAPI goodness ===

Goal: Make it easy for WP contributors to use refbase deployments to add articles

Priority:

Status: not started

Progress: 0%

Description: WP's citation templates are pretty straightforward clips of text, a'la:
 &lt;nowiki&gt;{{cite journal | author = Greiner C, Oppenheimer SM, Dunand DC | title = High strength, low stiffness, porous NiTi with superelastic properties. | journal = Acta Biomater | volume = 1 | issue = 6 | pages = 705-16 | year = 2005 | id = PMID 16701851}}&lt;/nowiki&gt;
[http://www.hubmed.org/ Hubmed] has a good example of UnAPIed Wikipedia citation generation.  They also have del.icio.us bookmarking (I guess we could add less obtrusive citeulike/connotea/etc. links this way).


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    <text bytes="24554" xml:space="preserve">This page lists planned feature additions:

'''Important''': Please note that the items listed below are simply suggestions for improving refbase and that we cannot (and don't want to) speculate on whether or when any of the listed features will be added to refbase.

== General ==

=== Resource types ===

Goal: Increase number of supported resource types.

Priority: 6

Status: added types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Report, Patent, Software

Progress: 50%

Description: refbase should allow users to choose from a variety of additional resource types including conference proceeding, patent, report, newspaper article, computer program, etc. All these types should invoke appropriate output on citation. In addition, the admin should be allowed to add additional resource types and users should be able to disable any unused types.

=== Migrate to more common libraries ===

Goal: To work under a larger number of configurations &amp; to depend on only well-maintained code.

Priority: 3

Status: not started

Progress: 0%

Description: We should consider migrating away from the ActiveLink XML library, as it isn't maintained. refbase should also be able to use MySQLi.

== Installation and updates ==

=== Redirect from ''index.php'' to ''install.php'' or ''update.php'' ===

Goal: refbase should direct to ''install.php'' or ''update.php'' as needed.

Priority: 6

Status: not started

Progress: 0%

Description: If the database doesn't exist, refbase should direct to ''install.php''. A version number or date for refbase could be stored in the database. If it is older than a version variable in ''index.php'', ''index.php'' could redirect to the update script.

=== Improvements to ''install.php'' ===

Goal: The ''install.php'' script should verify required server settings and provide more options for installation on different server setups.

Priority: 6

Status: not started

Progress: 0%

Description: 1) ''install.php'' should check required server settings prior to installation, and report possible problems in advance. 2) ''install.php'' should allow for installation into an existing database by providing an option for a table prefix that will be used for the refbase MySQL tables (currently, this can only be done by editing some configuration files). 3) To allow for web-based installation on shared hosts, ''install.php'' could offer an option to use an existing MySQL user (instead of setting up its own MySQL user which requires a MySQL admin user &amp; password). 4) ''install.php'' should provide an option to omit the sample data, i.e. install with a blank database.

=== Allow editing of configuration scripts through a web interface ===

Goal: Offer a web interface to the settings provided in ''ini.inc.php'', ''db.inc.php' and other config files.

Priority: 3

Status: not started

Progress: 0%

Description: Upon installation or update, refbase could list the settings in the various configuration files that are now manually edited &amp; allow users to make changes with the web interface.

== Searching ==

=== Search for duplicates ===

Goal: Offer the user means for handling duplicate database entries.

Priority: 4

Status: in development

Progress: 40%

Description: The database should offer means to easily spot duplicate entries and mark particular records as original (or duplicate) entry. Search features should allow users to exclude duplicate entries from the results list. It would be preferable if a smart dup detection mechanism such as phonetic matching could be used. See the [http://dev.mysql.com/doc/refman/4.1/en/string-functions.html MySQL string functions] &lt;code&gt;SOUNDEX&lt;/code&gt; and &lt;code&gt;SOUNDS LIKE&lt;/code&gt;.

=== ''OR'' search capabilities ===

Goal: Allow ''OR'' searches via the GUI.

Priority: 3

Status: not started

Progress: 0%

Description: When searching via one of the dedicated search pages, users should be able to specify whether a search on multiple fields will invoke an ''AND'' or an ''OR'' query (currently, entering search terms in multiple fields will always connect search terms with ''AND''). In addition, the "Search within Results" query form should allow users to expand the current result set, i.e. add found results to the existing list of results.

=== Simple handling of accented characters or umlauts ===

Goal: Allow naive users to search for accented characters by using the unaccented character and vice-versa.

Priority: 3

Status: not started

Progress: 0%

Description: If a search query contains no accents, it might be desirable to automatically search for commonly accented characters (especially in the Quick and Simple searches). If a user enters 'Jon', refbase could search for 'J[oÛˆ¯]n'. Similarly, it might be desirable to search for unaccented characters if a query contains an accent. If a user entered in 'JÛn', refbase might search instead for 'J[oÛ]n'. Naturally, there should be a mechanism for "advanced users" to have exact searches (perhaps by requiring a pre or post fix for more precise handling of (un)accented search strings.

=== Cross-site searches ===

Goal: Allow users to search and display results from other databases.

Priority: 2

Status: not started

Progress: 0%

Description: refbase should allow for cross-site searches both through other installations of refbase as well as through other bibliographic databases of the [http://bibliophile.sourceforge.net/ Bibliophile initiative]. Support for web service protocols such as [[Search/Retrieve_web_services|SRU]] and [[#OpenSearch support|OpenSearch]] will ease communication between different applications.

== Adding/Editing of records ==

=== Import ===

Goal: Offer direct data import from MODS XML.

Priority: 6

Status: not started

Progress: 0%

Description: refbase currently offers a number of native import scripts, as well as scripts which use [[Bibutils]] to convert formats to something which refbase can read. Long-term plans are to provide native import capabilities for [http://www.loc.gov/standards/mods/ MODS XML]. [[Importing records]] describes the import functionality available in refbase and future plans on import.

=== Direct import via arXiv ID ===

Goal: Use arXiv API to directly fetch and import records &amp; PDFs from arXiv.org.

Priority: 5

Status: import from arXiv.org has been fully implemented, though some aspects (such as parsing of the "Journal Ref" string) might need some further testing and fine-tuning

Progress: 95%

Description: refbase allows to directly fetch and import records from [http://www.pubmed.gov PubMed.gov] via their PubMed ID. A similar feature should be added for the [http://www.arxiv.org/ arXiv.org] e-Print archive. The [http://export.arxiv.org/api_help/docs/user-manual.html arXiv API] allows for HTTP GET queries by arXiv ID and returns OpenSearch Atom feeds with basic metadata (title, author(s), publication date, abstract, and journal info if given) and any URLs (HTML, PDF, DOI) associated with an article. refbase should parse the OpenSearch response and add new database records for each feed entry. Ideally, associated PDFs would be fetched as well and stored with the record.

=== Record-type specific forms ===

Goal: Simplify manual data input by providing record-type specific forms.

Priority: 2

Status: not started

Progress: 0%

Description: Record-type specific forms would guide a user by only showing those fields that are required for a particular record-type (like journal articles, book chapters or whole books). Record-type specific forms might not be necessary if the current "Add/Edit Record" form would be able to dynamically indicate required fields for a given record-type.

=== Input validation ===

Goal: refbase should dynamically validate input in the "Add/Edit Record" form.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should provide on-the-fly validation of data while a user inputs or edits data in the "Add/Edit Record" form. This would help users to ensure correct formatting for fields that require a specific string formatting (such as the ''author'' field). Dynamic form input validation may be best realized using [http://en.wikipedia.org/wiki/AJAX AJAX] style methods.

=== Auto-filling of fields ===

Goal: refbase should auto-fill fields if possible.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should be able to auto-fill empty fields based on information available in other fields and/or tables. This is especially useful if a flat database design is maintained. A typical application would be the auto-filling of journal-related fields (e.g. ''publisher'', ''place'', ''abbrev_journal'', ''language'' or ''summary_language'') from a journal database if the journal name (or ISSN) can be uniquely matched. If no journal info is available in the refbase journal database, a public service such as http://journalseek.net/ could be used for information retrieval and the fetched journal data could be automatically added to refbase's own journal database. Similarly, refbase could use web services from CrossRef (see [http://hublog.hubmed.org/archives/001624.html HubLog post] and links therein), WorldCat ([http://xissn.worldcat.org/xissnadmin/index.htm xISSN] &amp; [http://www.worldcat.org/affiliate/webservices/xisbn/app.jsp xISBN]) or LibraryThing ([http://www.librarything.com/thingology/2006/06/introducing-thingisbn_14.php thingISBN]) to supplement record metadata.

=== Auto-completion of field input ===

Goal: refbase should auto-complete user input in the "Add/Edit Record" form.

Priority: 4

Status: auto-completion has been fully implemented for the "Add/Edit Record" form and search suggestions are provided in some of the search forms (but they're not yet available in the "Advanced Search" and "Library Search" forms)

Progress: 95%

Description: It would be helpful if refbase would offer auto-completion features for fields of the "Add/Edit Record" form. This would allow users to start typing a string, then choose from a list of matching values (such as authors, keywords or journal names) that already exist in the database. Ideally, such a feature would not interfere with browser-specific auto-completion features and would be platform/browser agnostic. One way of implementing this would be a pop-up window where a generic database value browser would be combined with "Search within Results" functionality, and selected values would be written/appended to the field that's currently selected in the "Add/Edit Record" form.

=== Multiple files per record ===

Goal: refbase should allow users to upload multiple files per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to upload one file per record. It would be useful if multiple files could be attached to a given record. This would allow users to upload different representations, variants or versions of the same publication. Besides the final PDF, users could then attach a Powerpoint presentation or an audio file of an associated talk (though, in a strictly hierarchical design, talks or posters may warrant different but related records). Other use cases could be the upload of supplementary material or different manuscript revisions during collaborative preparation of an article, or the upload of a publicly available Open Access version (such as preprints or postprints). Upon upload, users should be able to specify file info (such as file type, language or a description) and access permissions individually for each file.

=== Multiple URLs per record ===

Goal: refbase should allow users to specify multiple URLs per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to specify one URL per record. It would be useful if multiple URLs could be added to a given record. While the primary URL could point to the publication's entry at the publisher site, additional URLs could point to, say, further info/news about the publication, any supplementary material, or related discussion located elsewhere. As is true for multiple files, some options to categorize and/or describe the given URLs as well as individual access permissions might be useful.

=== Support foreign record identifiers ===

Goal: refbase should support record identifiers from foreign repositories (e.g. from [http://www.pubmed.gov PubMed.gov] or [http://www.arxiv.org/ arXiv.org]) explicitly, and auto-generate links back to these repositories.

Priority: 5

Status: not started

Progress: 0%

Description: Upon import, refbase currently puts foreign record identifiers (such as IDs from arXiv, ISI Web of Science, PubMed, or SciFinder) into the ''notes'' field. It would be nice, however, if these record identifiers would be stored in some dedicated field(s). This would allow refbase to auto-generate links back to the corresponding record entries at the foreign repositories.

== Sharing ==

=== Public groups (tags) ===

Goal: Allow users to collectively share and categorize groups of records.

Priority: 6

Status: not started

Progress: 0%

Description: We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system.

=== User comments ===

Goal: Allow users to comment on particular records and exchange their thoughts with others.

Priority: 3

Status: not started

Progress: 0%

Description: We imagine a comment system where multiple comments would be allowed for a particular record and where comments could be made public, group-specific or private. Comments could be searched and displayed similar to (and in combination with) bibliographic references. Here's an ASCII mockup of how we envision such a system:

 +-------------------------------------------------------------------+
 |                                                                   |
 |  Cota GF, Horne EPW (1989) Physical control of Arctic ice algal   |
 |  production. Mar Ecol Prog Ser 52(2):111-121                      |
 |                                                                   |
 |  Matthias Steffens  |  This is an essential article that provides |
 |  *****              |  a good dataset on environmental control of |
 |  2005-04-27 23:33   |  primary production in polar areas.         |
 |                                                                   |
 +-------------------------------------------------------------------+
 |                                                                   |
 |  Mock T (2002) In situ primary production in young Antarctic sea  |
 |  ice. Hydrobiologia 470(1-3):127-132                              |
 |                                                                   |
 |  Matthias Steffens  |  Given the inaccessibility of the location  |
 |  ***                |  it's valuable data nonetheless. In situ    |
 |  2004-12-18 16:05   |  measurements are still very rare.          |
 |                                                                   |
 |  Paul Miller        |  I didn't get the point of this article.    |
 |  *                  |  IMHO, it's based on a weak dataset and     |
 |  2004-12-03 12:19   |  the conclusions are fuzzy.                 |
 |                                                                   |
 |  Matthias Steffens  |  Did anybody read this one? I'd appreciate  |
 |                     |  your opinions on the used method and       |
 |  2004-12-01 11:22   |  how this relates to existing methods.      |
 |                                                                   |
 +-------------------------------------------------------------------+

According to the above visualization, comments would print below the reference they are referring to. The reference would be displayed as a citation. Multiple citations with multiple comments could be displayed and you could search within results as usual. Note the stars which indicate the users rating. Users could edit/delete their own comments and decide who'll be able to see them (everyone, certain group(s) or private).

=== Better integration with desktop reference managers ===

Goal: Provide means for easy download of records to desktop reference managers, and for direct record upload to a refbase database.

Priority: 5

Status: for [http://www.sonnysoftware.com/ Bookends], "Upload to refbase" functionality has been added

Progress: 5%

Description: refbase should integrate with desktop reference managers (such as [http://bibdesk.sourceforge.net/ BibDesk], [http://www.sonnysoftware.com/ Bookends], [http://jabref.sourceforge.net/ JabRef], [http://mekentosj.com/papers/ Papers] or [http://www.zotero.org/ Zotero]) so that records stored in a refbase database can be easily retrieved from within these applications. Zotero can already extract bibliographic metadata from refbase's web pages via [[COinS]] or [[unAPI service|unAPI]], and something similar could work for other apps that feature web views. In addition, it would be desirable if users could search an online refbase database from within their desktop reference managers. The refbase search &amp; retrieve webservices offer standardized APIs for this, such as the [[Search/Retrieve_web_services|SRU/W webservice]] or [[#OpenSearch support|OpenSearch]] in conjunction with the existing [[unAPI service]]. Finally, it would be also useful if users of desktop reference managers could upload (and eventually synch) records to a refbase server directly from within their desktop application. In case of Zotero, "upload to refbase" functionality could be developed via an [http://dev.zotero.org/docs/sample_utility Zotero utility].

== Webservices ==

=== OpenSearch support ===

Goal: Allow OpenSearch clients to query refbase and return found results in OpenSearch response format.

Priority: 6

Status: OpenSearch support has been implemented with support for auto-discovery, multiple response formats (HTML, Atom, RSS, SRW_DC XML, SRW_MODS XML), simple CQL searches and support for search suggestions (returned in JSON or HTML); a better CQL parser would be desirable

Progress: 95%

Description: Similar to the refbase [[Search/Retrieve_web_services|SRU/W webservice]], refbase should support an [[OpenSearch service|OpenSearch]] webservice. OpenSearch capable clients would be able to [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_Query_element query] a refbase database and retrieve search results in an OpenSearch [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_response_elements response format], e.g. RSS 2.0 or Atom 1.0, plus the OpenSearch response extensions. This would also allow to integrate several refbase servers (or other OpenSearch capable servers) via [[Planned_feature_additions#Cross-site_searches|cross-site searches]]. When implemented, refbase should support auto-discovery to allow for [http://developer.mozilla.org/en/docs/Creating_OpenSearch_plugins_for_Firefox search plugins]. Eventual support for JSON for fetching of search suggestions would be nice.

=== API ===

Goal: Provide an API that allows clients to query a refbase database, retrieve results in a structured format and modify any database information.

Priority: 5

Status: not started

Progress: 0%

Description: Opposed to pure search/retrieve webservices (such as [[Search/Retrieve_web_services|SRU/W]] and [[OpenSearch service|OpenSearch]]), a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] API should also allow clients to send requests that ''alter'' the database, i.e. add, edit or delete records, meta-data or users. This will allow for easy integration with third-party tools and enable the development of alternative interfaces to a refbase database. It would be desirable to support an existing framework such as Google's [http://code.google.com/apis/gdata/index.html GData], [http://www.ukoln.ac.uk/repositories/digirep/index/SWORD SWORD] (Simple Web-service Offering Repository Deposit), or the [http://www.loc.gov/standards/sru/record-update/ Record Update service] that is proposed by the SRU community.

=== OAI Protocol for Metadata Harvesting ===

Goal: Provide (yet another) standard way for software to retrieve information from refbase. Eventually provide a mechanism for retrieval from arxiv/dspace/eprints, and other software which is targeted at larger institutions.

Priority: 5

Status: implemented support for the simple/unqualified Dublin Core (OAI_DC) XML format which is a prerequisite for OAI-PMH

Progress: 10%

Description: [http://www.openarchives.org/OAI/openarchivesprotocol.html The Open Archives Initiative Protocol for Metadata Harvesting], which is implemented by [http://software.eprints.org/ EPrints] and [http://www.dspace.org/ DSpace] uses Dublin Core XML over HTTP. This is harvested by google and yahoo and others.

== Citation support ==

=== Increase number of available citation styles ===

Goal: Add most commonly used citation styles and generally increase the number of available styles.

Priority: 6

Status: added styles: AMA, APA, Chicago, Harvard (3 variants), MLA, Vancouver

Progress: 75%

Description: By default, refbase should include at least the most universal styles (i.e. APA, MLA, Chicago, Harvard, Turabian, CB, CGOS, CBE, AMA). Besides that, it would be nice to increase the list of available citation styles substantially.

=== User-customizable citation styles ===

Goal: Allow users to create custom citation styles, preferably via the use of a plugin structure.

Priority: 4

Status: not started

Progress: 0%

Description: Currently, citation styles are defined as PHP functions which is very powerful but not very user friendly. We plan to enhance the cite feature by adding support for other (more general) citation formats. We'd like to integrate refbase with other solutions which offer users an easier way of adding or editing any citation styles. Projects such as Mark Grimshaw's [http://sourceforge.net/project/showfiles.php?group_id=113285&amp;package_id=150961 OSBib] or [http://xbiblio.sourceforge.net/ xbiblio] developed by Bruce D'Arcus come to mind. Some implementation of CSL (backed by Bruce and used by Zotero) would be nice.

== Export ==

== Access permissions ==

=== Record-specific permissions ===

Goal: Offer fine-grained access control on record-level.

Priority: 6

Status: not started

Progress: 0%

Description: The creator (or the admin) of a record should be able to specify who will be allowed to view a particular record. For each record, an authorized user should be able to set the record visibility to everyone, private or to particular groups of database users. Separate access control settings should be provided for file downloads and edits.

== Metadata and Microformats ==

=== Embedded RDF ===

Goal: Embed citation metadata in HTML pages as machine-readable RDF which may be processed by clients.

Priority: 5

Status: not started

Progress: 0%

Description: [http://en.wikipedia.org/wiki/Resource_Description_Framework RDF] is less supported than [[COinS]], but is a useful alternative that has some advantages (such as multiple author support). This will allow client-side tools (such as [http://www.zotero.org/ Zotero]) to more easily use the data provided by refbase.

=== Other microformats? ===

Goal: Other formats may be useful as well

Priority: 1

Status: not started

Progress: 0%

Description: [http://microformats.org/wiki/citation Other citation microformats] and a [http://microformats.org/wiki/search-results-example search results microformat] might eventually be useful. It seems like COinS is the most useful at this point in time, though.

=== Wikipedia citations &amp; other UnAPI goodness ===

Goal: Make it easy for WP contributors to use refbase deployments to add articles

Priority:

Status: not started

Progress: 0%

Description: WP's citation templates are pretty straightforward clips of text, a'la:
 &lt;nowiki&gt;{{cite journal | author = Greiner C, Oppenheimer SM, Dunand DC | title = High strength, low stiffness, porous NiTi with superelastic properties. | journal = Acta Biomater | volume = 1 | issue = 6 | pages = 705-16 | year = 2005 | id = PMID 16701851}}&lt;/nowiki&gt;
[http://www.hubmed.org/ Hubmed] has a good example of UnAPIed Wikipedia citation generation.  They also have del.icio.us bookmarking (I guess we could add less obtrusive citeulike/connotea/etc. links this way).


[[Category:General]]
__NOEDITSECTION__</text>
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</page>
<page arvcontinue="">
  <title>refbase:Site support</title>
  <ns>4</ns>
  <id>15</id>
  <revision>
    <id>40</id>
    <timestamp>2023-10-25T22:08:46Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 05-Jan-2007</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="404" xml:space="preserve">You're welcome to donate to our project!

== Donations ==

20% of your donation will be given to organizations that support the Open Source community. The remaining 80% will help us to fund development time and resources (e.g., server space &amp; traffic) expended for the refbase project.

Your support is much appreciated!

'''[http://sourceforge.net/project/project_donations.php?group_id=64647 Donate]'''</text>
    <sha1>6cdfdafc3a7a2d9a0294764d8d7a7fbd1a7fe277</sha1>
  </revision>
  <revision>
    <id>41</id>
    <parentid>40</parentid>
    <timestamp>2023-10-25T22:09:44Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="423" xml:space="preserve">You're welcome to donate to our project!

== Donations ==

20% of your donation will be given to organizations that support the Open Source community. The remaining 80% will help us to fund development time and resources (e.g., server space &amp; traffic) expended for the refbase project.

Your support is much appreciated!

'''[http://sourceforge.net/project/project_donations.php?group_id=64647 Donate]'''

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</page>
<page arvcontinue="">
  <title>More detailed introduction</title>
  <ns>0</ns>
  <id>16</id>
  <revision>
    <id>52</id>
    <timestamp>2023-10-26T11:44:26Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 19-Mar-2012</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1483" xml:space="preserve">This is a short introduction to "refbase", an
initiative that originated at the Institute for
Polar Ecology ([http://www.uni-kiel.de/ipoe/ IPOE]) at the University of Kiel (northern Germany)
under the initiative and auspices of Matthias Steffens.

At our institute, we felt the need to develop a web-based solution
for managing scientific literature, references and citations.
Aims are to develop a web-based, platform-independent,
multi-user application for literature databases based on php
and mysql.

An implementation that aims to provide a comprehensive and
platform-independent literature resource for scientists working
in the field of polar &amp; marine sciences can be reviewed at:

https://refbase.ipoe.uni-kiel.de/refs/

However, among the goals of this project is to adhere to web standards
(i.e. produce standards compliant html code), avoid cookies (if
possible) and make only sparse use of stuff like javascript - in
short: keep things simple and accessible.

The database application offers:

*a clean &amp; standardized interface
*a multitude of search options, including both, simple &amp; advanced as well as powerful SQL search options
*various display &amp; export options
*easy-to-use and platform indipendent in-text-citation


We realize that there are similar initiatives in the workings,
but we felt the need to develop a custom solution that would
really fit our own needs.

Just have a look and you will see the power of [http://refbase.net refbase].

[[Category:About]]</text>
    <sha1>9be98a08273d2964662614dcdfc07946595db341</sha1>
  </revision>
  <revision>
    <id>53</id>
    <parentid>52</parentid>
    <timestamp>2023-10-26T11:54:12Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Replaces link to (now defunct) Institute for Polar Ecology with a link to a German publication outlining the Institute's history</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1478" xml:space="preserve">This is a short introduction to "refbase", an
initiative that originated at the [//epic.awi.de/id/eprint/34903/ Institute for Polar Ecology] at the University of Kiel (northern Germany)
under the initiative and auspices of Matthias Steffens.

At our institute, we felt the need to develop a web-based solution
for managing scientific literature, references and citations.
Aims are to develop a web-based, platform-independent,
multi-user application for literature databases based on php
and mysql.

An implementation that aims to provide a comprehensive and
platform-independent literature resource for scientists working
in the field of polar &amp; marine sciences can be reviewed at:

https://refbase.ipoe.uni-kiel.de/refs/

However, among the goals of this project is to adhere to web standards
(i.e. produce standards compliant html code), avoid cookies (if
possible) and make only sparse use of stuff like javascript - in
short: keep things simple and accessible.

The database application offers:

*a clean &amp; standardized interface
*a multitude of search options, including both, simple &amp; advanced as well as powerful SQL search options
*various display &amp; export options
*easy-to-use and platform indipendent in-text-citation


We realize that there are similar initiatives in the workings,
but we felt the need to develop a custom solution that would
really fit our own needs.

Just have a look and you will see the power of [http://refbase.net refbase].

[[Category:About]]</text>
    <sha1>c47b08d44ebc72af6d502351b86f27767af43ecc</sha1>
  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Main Page</title>
  <ns>0</ns>
  <id>2</id>
  <revision>
    <id>54</id>
    <parentid>49</parentid>
    <timestamp>2023-10-26T12:06:22Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Removes link to "detailed introduction" about refbase from the main page (it's still available on the About page)</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1569" xml:space="preserve">&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt;
&lt;/div&gt;


== About refbase ==

[https://sourceforge.net/projects/refbase/ refbase] is a web-based, standards-compliant, multi-user interface for managing scientific literature &amp; bibliographic references. Based on [http://www.php.net/ php] &amp; [http://www.mysql.com/ mysql], it offers a bibliography database with powerful search tools and automatically generated citation lists.

== Download ==

You can [https://sourceforge.net/projects/refbase/files/latest/download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [https://sourceforge.net/p/refbase/code checked out] and [[SVN_version|installed]] from the refbase Subversion repository.

== Documentation ==

Please see the main [[Documentation]] page for available documentation, useful tips and troubleshooting guidance.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the docs or want to discuss new or existing features please use our [[refbase:Community_portal|forums or mailing lists]]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

There is a [[feature request|place]] to leave some ideas for future developments. If you like to discuss it, please use the forums on sourceforge.

__NOTOC__
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  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Feature request</title>
  <ns>0</ns>
  <id>17</id>
  <revision>
    <id>55</id>
    <timestamp>2023-10-26T12:16:19Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 15-Jun-2006</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1047" xml:space="preserve">Please see our wiki page on [[Planned_feature_additions|planned feature additions]]. If you don't find your feature suggestion there, feel free to add your suggestions below or use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum] on SourceForge.

== More reference links ==

Background: sometimes/often it is needed to find more information about references in the web (e.g. who cited the article, is there any .pdf outside etc.). Up to now, one has to copy the desired fields into the search engines (google und co). It could be helpful to have additional links on the details page for:

* Google
* Google Schoolar
* ISI Web of Sciences

* Mailto: author (a dedicated email-adress field could be helpful)

Daniel


== Easier creation of new users ==

When creating a new user, often information has to be added, which is the same, as for existing users (institution, address etc.). Therefore it would be nice if one could take over infos from existing users when adding new users.

Daniel


[[Category:General]]</text>
    <sha1>61881a471c00694ef14bc7e8e2f9d05203e5f83e</sha1>
  </revision>
  <revision>
    <id>56</id>
    <parentid>55</parentid>
    <timestamp>2023-10-26T12:20:23Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1064" xml:space="preserve">Please see our wiki page on [[Planned_feature_additions|planned feature additions]]. If you don't find your feature suggestion there, feel free to add your suggestions below or use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum] on SourceForge.

== More reference links ==

Background: sometimes/often it is needed to find more information about references in the web (e.g. who cited the article, is there any .pdf outside etc.). Up to now, one has to copy the desired fields into the search engines (google und co). It could be helpful to have additional links on the details page for:

* Google
* Google Schoolar
* ISI Web of Sciences

* Mailto: author (a dedicated email-adress field could be helpful)

Daniel

== Easier creation of new users ==

When creating a new user, often information has to be added, which is the same, as for existing users (institution, address etc.). Therefore it would be nice if one could take over infos from existing users when adding new users.

Daniel


[[Category:General]]
__NOEDITSECTION__</text>
    <sha1>50bd07e8c764e94f0b5c0b5166dc2995302c2477</sha1>
  </revision>
  <revision>
    <id>57</id>
    <parentid>56</parentid>
    <timestamp>2023-10-26T12:23:00Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Prefer the Feature Requests forum (opposed to adding feature requests directly to this wiki)</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1028" xml:space="preserve">Please see our wiki page on [[Planned_feature_additions|planned feature additions]]. If you don't find your feature suggestion there, please use our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum] on SourceForge.

== More reference links ==

Background: sometimes/often it is needed to find more information about references in the web (e.g. who cited the article, is there any .pdf outside etc.). Up to now, one has to copy the desired fields into the search engines (google und co). It could be helpful to have additional links on the details page for:

* Google
* Google Schoolar
* ISI Web of Sciences

* Mailto: author (a dedicated email-adress field could be helpful)

Daniel

== Easier creation of new users ==

When creating a new user, often information has to be added, which is the same, as for existing users (institution, address etc.). Therefore it would be nice if one could take over infos from existing users when adding new users.

Daniel


[[Category:General]]
__NOEDITSECTION__</text>
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  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>refbase:Community portal</title>
  <ns>4</ns>
  <id>10</id>
  <revision>
    <id>58</id>
    <parentid>17</parentid>
    <timestamp>2023-10-26T12:34:47Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>For email, expose a general mailto address instead of the wiki's email functionality (which would require users to login)</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1551" xml:space="preserve">We like to hear from you!

== Help ==

If you've got questions or encounter any problems using refbase you're welcome to use our [https://sourceforge.net/p/refbase/discussion/218758/ help forum] or submit your feedback to our [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Discuss ==

If you need assistance from other users, want to share tips or discuss existing or potential features you're welcome to browse, search or post to our [https://sourceforge.net/p/refbase/discussion/218757/ discussion forum] or the [http://lists.sourceforge.net/lists/listinfo/refbase-talk refbase-talk mailinglist].

== Feature Requests ==

If you've got some suggestions how refbase can be improved you're welcome to share your ideas [[feature request|here]]. Alternatively, you can use our [https://sourceforge.net/p/refbase/discussion/351913/ Feature Requests forum] to request or discuss any new features. You may be also interested in our list of [[Planned_feature_additions|planned features]].

== Get Involved ==

If you'd like to contribute to the ongoing development of refbase please send us an [mailto:info@refbase.net email]. For bugs or feature requests please use our [https://sourceforge.net/p/refbase/discussion/ forums] or [https://sourceforge.net/p/refbase/mailman/ mailinglists]. If you'd like to contribute to this wiki please see our [[Help:Contents|help section]] for more information on editing of pages.

You can also [mailto:info@refbase.net contact us directly via email].
__NOTOC__
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  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Help:Contents</title>
  <ns>12</ns>
  <id>18</id>
  <revision>
    <id>59</id>
    <timestamp>2023-10-26T12:43:25Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 07-Jan-2007</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1471" xml:space="preserve">We encourage you to contribute to this wiki!

We ask you to [[Special:Userlogin|login]] if you're going to edit or add pages to the this wiki. If you have no account yet you can easily [[Special:Userlogin|create a user account]]. After you've created your personal account, please don't forget to specify a contact email address in your [[Special:Preferences|account preferences]].

See the links below to learn more about editing of pages:

* [http://en.wikipedia.org/wiki/Wikitext Wikipedia on wikitext]
* [http://meta.wikimedia.org/wiki/Help:Editing Wikimedia: Editing overview]
* [http://meta.wikimedia.org/wiki/Help:Html_in_wikitext Wikimedia: Use of HTML in wikitext]
* [http://meta.wikimedia.org/wiki/Help:Starting_a_new_page Wikimedia: Starting a new page]

More info is available at the [http://meta.wikimedia.org/wiki/MediaWiki_User%27s_Guide MediaWiki User's Guide].


When creating screenshots from the refbase-interface, external programs could be helpful, which store screenshots directly in files. The following list represents programs, which are used so far:
* [http://sourceforge.net/projects/smartision-sc smartision screencapture] - for Win32 systems
* [http://www.donationcoder.com/Software/Mouser/screenshotcaptor/index.html Screenshot Captor] - extremely powerful screencapture program for Win32 systems. Has the ability to directly add arrows and highlights to your screenshot, before saving the image


We appreciate your contributions, have fun!</text>
    <sha1>1b4ed9c37f9ce205966a0b43241a28c6c012270a</sha1>
  </revision>
  <revision>
    <id>60</id>
    <parentid>59</parentid>
    <timestamp>2023-10-26T12:51:27Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>User account creation is only available on request</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1461" xml:space="preserve">We encourage you to contribute to this wiki!

We ask you to [[Special:Userlogin|login]] if you're going to edit or add pages to this wiki. If you have no account yet you can [[refbase:Community_portal|request]] to have one created for you. After you've logged in, please don't forget to specify a contact email address in your [[Special:Preferences|account preferences]].

See the links below to learn more about editing of pages:

* [http://en.wikipedia.org/wiki/Wikitext Wikipedia on wikitext]
* [http://meta.wikimedia.org/wiki/Help:Editing Wikimedia: Editing overview]
* [http://meta.wikimedia.org/wiki/Help:Html_in_wikitext Wikimedia: Use of HTML in wikitext]
* [http://meta.wikimedia.org/wiki/Help:Starting_a_new_page Wikimedia: Starting a new page]

More info is available at the [http://meta.wikimedia.org/wiki/MediaWiki_User%27s_Guide MediaWiki User's Guide].


When creating screenshots from the refbase-interface, external programs could be helpful, which store screenshots directly in files. The following list represents programs, which are used so far:
* [http://sourceforge.net/projects/smartision-sc smartision screencapture] - for Win32 systems
* [http://www.donationcoder.com/Software/Mouser/screenshotcaptor/index.html Screenshot Captor] - extremely powerful screencapture program for Win32 systems. Has the ability to directly add arrows and highlights to your screenshot, before saving the image


We appreciate your contributions, have fun!</text>
    <sha1>a64fdecc785228e5dcc6b8f4d50bffcfe0abf887</sha1>
  </revision>
  <revision>
    <id>61</id>
    <parentid>60</parentid>
    <timestamp>2023-10-26T13:02:42Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Updates section about creating screenshots</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1579" xml:space="preserve">We encourage you to contribute to this wiki!

We ask you to [[Special:Userlogin|login]] if you're going to edit or add pages to this wiki. If you have no account yet you can [[refbase:Community_portal|request]] to have one created for you. After you've logged in, please don't forget to specify a contact email address in your [[Special:Preferences|account preferences]].

See the links below to learn more about editing of pages:

* [http://en.wikipedia.org/wiki/Wikitext Wikipedia on wikitext]
* [http://meta.wikimedia.org/wiki/Help:Editing Wikimedia: Editing overview]
* [http://meta.wikimedia.org/wiki/Help:Html_in_wikitext Wikimedia: Use of HTML in wikitext]
* [http://meta.wikimedia.org/wiki/Help:Starting_a_new_page Wikimedia: Starting a new page]

More info is available at the [http://meta.wikimedia.org/wiki/MediaWiki_User%27s_Guide MediaWiki User's Guide].


When creating screenshots from the refbase interface, you may find the use of third-party utilities helpful. Following programs can be used on Win32 systems:
* [http://sourceforge.net/projects/smartision-sc smartision screencapture]
* [http://www.donationcoder.com/Software/Mouser/screenshotcaptor/index.html Screenshot Captor] - powerful screencapture program whch allows to add arrows and highlights to your screenshot
On macOS, press &lt;code&gt;command-shift-4&lt;/code&gt;, then select the region to be captured. Alternatively, to capture an entire window (incl. drop shadows), press &lt;code&gt;command-shift-4&lt;/code&gt;, then press &lt;code&gt;space&lt;/code&gt; and click into the window.


We appreciate your contributions, have fun!</text>
    <sha1>13294faa83fdfc9c02de4d3fa8015ef4b4060f5f</sha1>
  </revision>
  <revision>
    <id>62</id>
    <parentid>61</parentid>
    <timestamp>2023-10-26T13:11:56Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Updates MediaWiki help links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1568" xml:space="preserve">We encourage you to contribute to this wiki!

We ask you to [[Special:Userlogin|login]] if you're going to edit or add pages to this wiki. If you have no account yet you can [[refbase:Community_portal|request]] to have one created for you. After you've logged in, please don't forget to specify a contact email address in your [[Special:Preferences|account preferences]].

See the links below to learn more about editing of pages:

* [http://en.wikipedia.org/wiki/Wikitext Wikipedia on wikitext]
* [https://www.mediawiki.org/wiki/Help:Editing_pages MediaWiki: Editing pages]
* [https://www.mediawiki.org/wiki/Help:HTML_in_wikitext MediaWiki: Use of HTML in wikitext]
* [https://www.mediawiki.org/wiki/Help:Starting_a_new_page MediaWiki: Starting a new page]

More info is available at the [https://meta.wikimedia.org/wiki/Help:Contents MediaWiki handbook].


When creating screenshots from the refbase interface, you may find the use of third-party utilities helpful. Following programs can be used on Win32 systems:
* [http://sourceforge.net/projects/smartision-sc smartision screencapture]
* [http://www.donationcoder.com/Software/Mouser/screenshotcaptor/index.html Screenshot Captor] - powerful screencapture program whch allows to add arrows and highlights to your screenshot
On macOS, press &lt;code&gt;command-shift-4&lt;/code&gt;, then select the region to be captured. Alternatively, to capture an entire window (incl. drop shadows), press &lt;code&gt;command-shift-4&lt;/code&gt;, then press &lt;code&gt;space&lt;/code&gt; and click into the window.


We appreciate your contributions, have fun!</text>
    <sha1>2a092e61d26e1a8cd0a2682bfb34026de159fbc6</sha1>
  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Web Reference Database</title>
  <ns>0</ns>
  <id>3</id>
  <revision>
    <id>63</id>
    <parentid>39</parentid>
    <timestamp>2023-10-26T13:46:18Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update link to Community_Portal page</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2161" xml:space="preserve">
&lt;div align="center"&gt;
&lt;div id="refbase-badge"&gt;refbase&lt;/div&gt; &lt;br /&gt; 
'''web-based, platform-independent, &lt;br /&gt; multi-user interface for managing &lt;br /&gt; scientific literature &amp; citations'''
&lt;/div&gt;

== Features ==

refbase can import and export references in various formats (including BibTeX, Endnote, RIS, PubMed, ISI Web of Science, CSA Illumina, RefWorks, MODS XML, OpenOffice, and MS Word). It can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers powerful searching, and RSS support. Its OpenSearch and SRU/W web services, and support for unAPI &amp; COinS metadata allow for easy access by clients and search engines. Please see our [[Feature highlights]] page for a more detailed description of features. An overview of the major feature additions in refbase-0.9.5 is given [[Main_features#refbase-0.9.5|here]].

== Download ==

You can [https://sourceforge.net/projects/refbase/files/latest/download download] the stable release version of refbase from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page]. Please see the instructions on how to [[Installing_refbase|install]] or [[Updating_refbase|update]] refbase. The latest source code can be [https://sourceforge.net/p/refbase/code checked out] and [[SVN_version|installed]] from the refbase Subversion repository.

== Demo &amp; Documentation ==

We invite you to test-drive refbase at the [http://demo.refbase.net/ refbase Demo Database] (latest stable release version) or the [http://beta.refbase.net/ refbase Beta Database] (latest development version). Feel free to login and play around! Further demo and real-world installations are listed [[Refbase_users|here]]. For available documentation, useful tips and troubleshooting guidance, please see the main [[Documentation]] page.

== Help &amp; Discussion ==

If you've got questions which aren't covered in the [[Documentation|docs]], want to discuss new or existing features or want to get involved with the ongoing development of refbase please see our [[refbase:Community_portal|Community Portal]] for pointers to forums, mailing lists and contact information.

__NOTOC__ __NOEDITSECTION__</text>
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<page arvcontinue="20231026120622|54">
  <title>Installing refbase</title>
  <ns>0</ns>
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    <timestamp>2023-10-26T13:51:10Z</timestamp>
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    <comment>Original page content from 27-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6049" xml:space="preserve">This document describes how to install refbase.

== Web-based installation ==

This section describes how to install refbase using the install script (''install.php'') that comes with the refbase package. Alternative installation methods are described [[#Alternative_installation_methods|below]]. See the 'INSTALL' file that comes with the refbase package for latest information regarding the installation process.

=== Check requirements ===

Please make sure that your server meets the [[Requirements|requirements]].

=== Download and install scripts ===

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

Additionally, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended.

=== Configure database settings ===

Please be sure to [[Database_configuration|configure important database settings]] prior to installation. While you might be able to use the refbase package without modifying the default settings, we highly recommend not to use the default values.

=== Install refbase via ''install.php'' ===

Point your web browser to ''install.php'', and fill out and submit the install form(*) to complete the installation process.

(*) In case you're curious, the install form looks [http://beta.refbase.net/install.php like this].

Note that the install script currently requires a user with full access to the ''mysql'' database (more info [[#Additional_web-install_requirements|below]]). I.e., if you're trying to install refbase on a shared host with limited MySQL access privileges, you may need to perform a [[#Manual_installation|manual installation]] instead.

== Alternative installation methods ==

=== Manual installation ===

If you're experiencing problems with the web-based installation you can try a [[manual installation]] instead.

=== Gentoo Linux ===

[http://www.gentoo.org/ Gentoo] has an ebuild of refbase in [http://gentoo-portage.com/app-text/refbase portage], so you can merely:
 $ emerge refbase

=== Mandrake/Mandriva Linux ===

[http://club.mandriva.com/xwiki/bin/view/rpms/Application/refbase refbase RPMs] are available. RPMs for refbase-0.9.5 are available e.g. [ftp://ftp.free.fr/mirrors/ftp.mandriva.com/MandrivaLinux/devel/cooker/cooker/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here] and [ftp://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/devel/cooker/i586/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here]. To install the refbase RPM, use ''urpmi'' or ''rpmdrake'':

 $ urpmi refbase

then finish the installation by pointing your web browser to &lt;code&gt;&lt;nowiki&gt;http://localhost/refbase/install.php&lt;/nowiki&gt;&lt;/code&gt;

=== Virtual machine ===

You may use the gratis [http://www.vmware.com/products/player/ VMware Player] with a [http://www.vmware.com/appliances/directory/1272 refbase virtual appliance] (hosted by [http://arc.nucapt.northwestern.edu NUCAPT]).

=== WOS Portable ===

Windows users can download the free and open source [http://www.chsoftware.net/en/useware/wos/wos.htm WOS Portable] to have an Apache/MySQL/PHP stack (which can even be run from a USB stick).  The refbase package can reportedly be downloaded from their premium site.  Non-members can download [http://arc.nucapt.northwestern.edu/~karnesky/refbase/refbase.wos the refbase WOS package] from [http://arc.nucapt.northwestern.edu NUCAPT].

== Installation Troubleshooting ==

A list of possible problems and their solutions can be found in the [[Installation-Troubleshooting]] section.

== Installation over an existing database ==

In the install form, you will find a cautionary note:

 Note that, if there's already an existing database with the name specified
 in $databaseName, clicking the Install button will overwrite ALL data in that
 database!

Actually, this note is only true if you're installing into an '''existing refbase database'''. The refbase ''install.php'' script will NOT delete an existing database but will only overwrite those [[MySQL tables|tables]] in the specifed database that have names identical to the ones used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables.

In other words, if the table names in your existing database don't conflict with the table names used by refbase (or if you rename the refbase table names in ''db.inc.php'' AND in ''install.sql'' '''prior to installation''' so that they don't conflict with existing table names), then you should be able to use ''install.php'' for installation of refbase into any existing database.

However, it is a very good idea to make a [[Backup the database|full backup]] of your existing database prior to installation. Also, it may be worth to first do some testing with a non-critical database copy.

== Additional web-install requirements ==

In order to run the ''install.php'' script as described above, you will need a MySQL username with permission to modify the database named ''mysql'' which stores the MySQL [http://dev.mysql.com/doc/refman/5.0/en/what-privileges.html user privilege] information. This is since the refbase install script adds a dedicated MySQL user to the ''mysql'' database which will be used with your refbase application ([[Add MySQL User|more info]]).

Some shared hosts do not provide MySQL usernames with the required permissions, but instead provide alternate interfaces for MySQL username administration such as a web-based control center. If you face this restriction, you will need to perform a [[#Manual_installation|manual installation]].

[[Category:Installation]]</text>
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  <revision>
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    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6067" xml:space="preserve">This document describes how to install refbase.

== Web-based installation ==

This section describes how to install refbase using the install script (''install.php'') that comes with the refbase package. Alternative installation methods are described [[#Alternative_installation_methods|below]]. See the 'INSTALL' file that comes with the refbase package for latest information regarding the installation process.

=== Check requirements ===

Please make sure that your server meets the [[Requirements|requirements]].

=== Download and install scripts ===

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

Additionally, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended.

=== Configure database settings ===

Please be sure to [[Database_configuration|configure important database settings]] prior to installation. While you might be able to use the refbase package without modifying the default settings, we highly recommend not to use the default values.

=== Install refbase via ''install.php'' ===

Point your web browser to ''install.php'', and fill out and submit the install form(*) to complete the installation process.

(*) In case you're curious, the install form looks [http://beta.refbase.net/install.php like this].

Note that the install script currently requires a user with full access to the ''mysql'' database (more info [[#Additional_web-install_requirements|below]]). I.e., if you're trying to install refbase on a shared host with limited MySQL access privileges, you may need to perform a [[#Manual_installation|manual installation]] instead.

== Alternative installation methods ==

=== Manual installation ===

If you're experiencing problems with the web-based installation you can try a [[manual installation]] instead.

=== Gentoo Linux ===

[http://www.gentoo.org/ Gentoo] has an ebuild of refbase in [http://gentoo-portage.com/app-text/refbase portage], so you can merely:
 $ emerge refbase

=== Mandrake/Mandriva Linux ===

[http://club.mandriva.com/xwiki/bin/view/rpms/Application/refbase refbase RPMs] are available. RPMs for refbase-0.9.5 are available e.g. [ftp://ftp.free.fr/mirrors/ftp.mandriva.com/MandrivaLinux/devel/cooker/cooker/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here] and [ftp://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/devel/cooker/i586/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here]. To install the refbase RPM, use ''urpmi'' or ''rpmdrake'':

 $ urpmi refbase

then finish the installation by pointing your web browser to &lt;code&gt;&lt;nowiki&gt;http://localhost/refbase/install.php&lt;/nowiki&gt;&lt;/code&gt;

=== Virtual machine ===

You may use the gratis [http://www.vmware.com/products/player/ VMware Player] with a [http://www.vmware.com/appliances/directory/1272 refbase virtual appliance] (hosted by [http://arc.nucapt.northwestern.edu NUCAPT]).

=== WOS Portable ===

Windows users can download the free and open source [http://www.chsoftware.net/en/useware/wos/wos.htm WOS Portable] to have an Apache/MySQL/PHP stack (which can even be run from a USB stick).  The refbase package can reportedly be downloaded from their premium site.  Non-members can download [http://arc.nucapt.northwestern.edu/~karnesky/refbase/refbase.wos the refbase WOS package] from [http://arc.nucapt.northwestern.edu NUCAPT].

== Installation Troubleshooting ==

A list of possible problems and their solutions can be found in the [[Installation-Troubleshooting]] section.

== Installation over an existing database ==

In the install form, you will find a cautionary note:

 Note that, if there's already an existing database with the name specified
 in $databaseName, clicking the Install button will overwrite ALL data in that
 database!

Actually, this note is only true if you're installing into an '''existing refbase database'''. The refbase ''install.php'' script will NOT delete an existing database but will only overwrite those [[MySQL tables|tables]] in the specifed database that have names identical to the ones used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables.

In other words, if the table names in your existing database don't conflict with the table names used by refbase (or if you rename the refbase table names in ''db.inc.php'' AND in ''install.sql'' '''prior to installation''' so that they don't conflict with existing table names), then you should be able to use ''install.php'' for installation of refbase into any existing database.

However, it is a very good idea to make a [[Backup the database|full backup]] of your existing database prior to installation. Also, it may be worth to first do some testing with a non-critical database copy.

== Additional web-install requirements ==

In order to run the ''install.php'' script as described above, you will need a MySQL username with permission to modify the database named ''mysql'' which stores the MySQL [http://dev.mysql.com/doc/refman/5.0/en/what-privileges.html user privilege] information. This is since the refbase install script adds a dedicated MySQL user to the ''mysql'' database which will be used with your refbase application ([[Add MySQL User|more info]]).

Some shared hosts do not provide MySQL usernames with the required permissions, but instead provide alternate interfaces for MySQL username administration such as a web-based control center. If you face this restriction, you will need to perform a [[#Manual_installation|manual installation]].

[[Category:Installation]]
__NOEDITSECTION__</text>
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    <comment>Update external links and remove dead links/info</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5327" xml:space="preserve">This document describes how to install refbase.

== Web-based installation ==

This section describes how to install refbase using the install script (''install.php'') that comes with the refbase package. Alternative installation methods are described [[#Alternative_installation_methods|below]]. See the 'INSTALL' file that comes with the refbase package for latest information regarding the installation process.

=== Check requirements ===

Please make sure that your server meets the [[Requirements|requirements]].

=== Download and install scripts ===

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

Additionally, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended.

=== Configure database settings ===

Please be sure to [[Database_configuration|configure important database settings]] prior to installation. While you might be able to use the refbase package without modifying the default settings, we highly recommend not to use the default values.

=== Install refbase via ''install.php'' ===

Point your web browser to ''install.php'', and fill out and submit the install form to complete the installation process.

Note that the install script currently requires a user with full access to the ''mysql'' database (more info [[#Additional_web-install_requirements|below]]). I.e., if you're trying to install refbase on a shared host with limited MySQL access privileges, you may need to perform a [[#Manual_installation|manual installation]] instead.

== Alternative installation methods ==

=== Manual installation ===

If you're experiencing problems with the web-based installation you can try a [[manual installation]] instead.

=== Gentoo Linux ===

[http://www.gentoo.org/ Gentoo] has an [https://gentoobrowse.randomdan.homeip.net/packages/app-text/refbase ebuild of refbase] in [https://wiki.gentoo.org/wiki/Portage portage], so you can merely:

 $ emerge refbase

=== Mandrake/Mandriva Linux ===

[https://rpmfind.net/linux/rpm2html/search.php?query=refbase refbase RPMs] are available. RPMs for refbase-0.9.5 are available e.g. [ftp://ftp.free.fr/mirrors/ftp.mandriva.com/MandrivaLinux/devel/cooker/cooker/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here] and [ftp://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/devel/cooker/i586/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here]. To install the refbase RPM, use ''urpmi'' or ''rpmdrake'':

 $ urpmi refbase

then finish the installation by pointing your web browser to &lt;code&gt;&lt;nowiki&gt;http://localhost/refbase/install.php&lt;/nowiki&gt;&lt;/code&gt;

== Installation Troubleshooting ==

A list of possible problems and their solutions can be found in the [[Installation-Troubleshooting]] section.

== Installation over an existing database ==

In the install form, you will find a cautionary note:

 Note that, if there's already an existing database with the name specified
 in $databaseName, clicking the Install button will overwrite ALL data in that
 database!

Actually, this note is only true if you're installing into an '''existing refbase database'''. The refbase ''install.php'' script will NOT delete an existing database but will only overwrite those [[MySQL tables|tables]] in the specifed database that have names identical to the ones used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables.

In other words, if the table names in your existing database don't conflict with the table names used by refbase (or if you rename the refbase table names in ''db.inc.php'' AND in ''install.sql'' '''prior to installation''' so that they don't conflict with existing table names), then you should be able to use ''install.php'' for installation of refbase into any existing database.

However, it is a very good idea to make a [[Backup the database|full backup]] of your existing database prior to installation. Also, it may be worth to first do some testing with a non-critical database copy.

== Additional web-install requirements ==

In order to run the ''install.php'' script as described above, you will need a MySQL username with permission to modify the database named ''mysql'' which stores the MySQL [https://dev.mysql.com/doc/refman/8.0/en/privileges-provided.html user privilege] information. This is since the refbase install script adds a dedicated MySQL user to the ''mysql'' database which will be used with your refbase application ([[Add MySQL User|more info]]).

Some shared hosts do not provide MySQL usernames with the required permissions, but instead provide alternate interfaces for MySQL username administration such as a web-based control center. If you face this restriction, you will need to perform a [[#Manual_installation|manual installation]].

[[Category:Installation]]
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  <revision>
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      <id>1</id>
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    <minor/>
    <comment>Update link to Gentoo refbase package</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5313" xml:space="preserve">This document describes how to install refbase.

== Web-based installation ==

This section describes how to install refbase using the install script (''install.php'') that comes with the refbase package. Alternative installation methods are described [[#Alternative_installation_methods|below]]. See the 'INSTALL' file that comes with the refbase package for latest information regarding the installation process.

=== Check requirements ===

Please make sure that your server meets the [[Requirements|requirements]].

=== Download and install scripts ===

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

Additionally, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended.

=== Configure database settings ===

Please be sure to [[Database_configuration|configure important database settings]] prior to installation. While you might be able to use the refbase package without modifying the default settings, we highly recommend not to use the default values.

=== Install refbase via ''install.php'' ===

Point your web browser to ''install.php'', and fill out and submit the install form to complete the installation process.

Note that the install script currently requires a user with full access to the ''mysql'' database (more info [[#Additional_web-install_requirements|below]]). I.e., if you're trying to install refbase on a shared host with limited MySQL access privileges, you may need to perform a [[#Manual_installation|manual installation]] instead.

== Alternative installation methods ==

=== Manual installation ===

If you're experiencing problems with the web-based installation you can try a [[manual installation]] instead.

=== Gentoo Linux ===

[http://www.gentoo.org/ Gentoo] has an [https://packages.gentoo.org/packages/app-text/refbase ebuild of refbase] in [https://wiki.gentoo.org/wiki/Portage portage], so you can merely:

 $ emerge refbase

=== Mandrake/Mandriva Linux ===

[https://rpmfind.net/linux/rpm2html/search.php?query=refbase refbase RPMs] are available. RPMs for refbase-0.9.5 are available e.g. [ftp://ftp.free.fr/mirrors/ftp.mandriva.com/MandrivaLinux/devel/cooker/cooker/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here] and [ftp://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/devel/cooker/i586/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here]. To install the refbase RPM, use ''urpmi'' or ''rpmdrake'':

 $ urpmi refbase

then finish the installation by pointing your web browser to &lt;code&gt;&lt;nowiki&gt;http://localhost/refbase/install.php&lt;/nowiki&gt;&lt;/code&gt;

== Installation Troubleshooting ==

A list of possible problems and their solutions can be found in the [[Installation-Troubleshooting]] section.

== Installation over an existing database ==

In the install form, you will find a cautionary note:

 Note that, if there's already an existing database with the name specified
 in $databaseName, clicking the Install button will overwrite ALL data in that
 database!

Actually, this note is only true if you're installing into an '''existing refbase database'''. The refbase ''install.php'' script will NOT delete an existing database but will only overwrite those [[MySQL tables|tables]] in the specifed database that have names identical to the ones used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables.

In other words, if the table names in your existing database don't conflict with the table names used by refbase (or if you rename the refbase table names in ''db.inc.php'' AND in ''install.sql'' '''prior to installation''' so that they don't conflict with existing table names), then you should be able to use ''install.php'' for installation of refbase into any existing database.

However, it is a very good idea to make a [[Backup the database|full backup]] of your existing database prior to installation. Also, it may be worth to first do some testing with a non-critical database copy.

== Additional web-install requirements ==

In order to run the ''install.php'' script as described above, you will need a MySQL username with permission to modify the database named ''mysql'' which stores the MySQL [https://dev.mysql.com/doc/refman/8.0/en/privileges-provided.html user privilege] information. This is since the refbase install script adds a dedicated MySQL user to the ''mysql'' database which will be used with your refbase application ([[Add MySQL User|more info]]).

Some shared hosts do not provide MySQL usernames with the required permissions, but instead provide alternate interfaces for MySQL username administration such as a web-based control center. If you face this restriction, you will need to perform a [[#Manual_installation|manual installation]].

[[Category:Installation]]
__NOEDITSECTION__</text>
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  </revision>
  <revision>
    <id>83</id>
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    <timestamp>2023-11-05T19:36:47Z</timestamp>
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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Change again link for Mandriva refbase RPMs</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5287" xml:space="preserve">This document describes how to install refbase.

== Web-based installation ==

This section describes how to install refbase using the install script (''install.php'') that comes with the refbase package. Alternative installation methods are described [[#Alternative_installation_methods|below]]. See the 'INSTALL' file that comes with the refbase package for latest information regarding the installation process.

=== Check requirements ===

Please make sure that your server meets the [[Requirements|requirements]].

=== Download and install scripts ===

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

Additionally, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended.

=== Configure database settings ===

Please be sure to [[Database_configuration|configure important database settings]] prior to installation. While you might be able to use the refbase package without modifying the default settings, we highly recommend not to use the default values.

=== Install refbase via ''install.php'' ===

Point your web browser to ''install.php'', and fill out and submit the install form to complete the installation process.

Note that the install script currently requires a user with full access to the ''mysql'' database (more info [[#Additional_web-install_requirements|below]]). I.e., if you're trying to install refbase on a shared host with limited MySQL access privileges, you may need to perform a [[#Manual_installation|manual installation]] instead.

== Alternative installation methods ==

=== Manual installation ===

If you're experiencing problems with the web-based installation you can try a [[manual installation]] instead.

=== Gentoo Linux ===

[http://www.gentoo.org/ Gentoo] has an [https://packages.gentoo.org/packages/app-text/refbase ebuild of refbase] in [https://wiki.gentoo.org/wiki/Portage portage], so you can merely:

 $ emerge refbase

=== Mandrake/Mandriva Linux ===

[https://pkgs.org/download/refbase refbase RPMs] are available. RPMs for refbase-0.9.5 are available e.g. [ftp://ftp.free.fr/mirrors/ftp.mandriva.com/MandrivaLinux/devel/cooker/cooker/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here] and [ftp://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/devel/cooker/i586/media/contrib/release/refbase-0.9.5-1mdv2009.1.noarch.rpm here]. To install the refbase RPM, use ''urpmi'' or ''rpmdrake'':

 $ urpmi refbase

then finish the installation by pointing your web browser to &lt;code&gt;&lt;nowiki&gt;http://localhost/refbase/install.php&lt;/nowiki&gt;&lt;/code&gt;

== Installation Troubleshooting ==

A list of possible problems and their solutions can be found in the [[Installation-Troubleshooting]] section.

== Installation over an existing database ==

In the install form, you will find a cautionary note:

 Note that, if there's already an existing database with the name specified
 in $databaseName, clicking the Install button will overwrite ALL data in that
 database!

Actually, this note is only true if you're installing into an '''existing refbase database'''. The refbase ''install.php'' script will NOT delete an existing database but will only overwrite those [[MySQL tables|tables]] in the specifed database that have names identical to the ones used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables.

In other words, if the table names in your existing database don't conflict with the table names used by refbase (or if you rename the refbase table names in ''db.inc.php'' AND in ''install.sql'' '''prior to installation''' so that they don't conflict with existing table names), then you should be able to use ''install.php'' for installation of refbase into any existing database.

However, it is a very good idea to make a [[Backup the database|full backup]] of your existing database prior to installation. Also, it may be worth to first do some testing with a non-critical database copy.

== Additional web-install requirements ==

In order to run the ''install.php'' script as described above, you will need a MySQL username with permission to modify the database named ''mysql'' which stores the MySQL [https://dev.mysql.com/doc/refman/8.0/en/privileges-provided.html user privilege] information. This is since the refbase install script adds a dedicated MySQL user to the ''mysql'' database which will be used with your refbase application ([[Add MySQL User|more info]]).

Some shared hosts do not provide MySQL usernames with the required permissions, but instead provide alternate interfaces for MySQL username administration such as a web-based control center. If you face this restriction, you will need to perform a [[#Manual_installation|manual installation]].

[[Category:Installation]]
__NOEDITSECTION__</text>
    <sha1>d05669cfad2b6d11407c364849d89a4afc1b7afc</sha1>
  </revision>
  <revision>
    <id>84</id>
    <parentid>83</parentid>
    <timestamp>2023-11-05T19:46:06Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update FTP download link for refbase RPM</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5141" xml:space="preserve">This document describes how to install refbase.

== Web-based installation ==

This section describes how to install refbase using the install script (''install.php'') that comes with the refbase package. Alternative installation methods are described [[#Alternative_installation_methods|below]]. See the 'INSTALL' file that comes with the refbase package for latest information regarding the installation process.

=== Check requirements ===

Please make sure that your server meets the [[Requirements|requirements]].

=== Download and install scripts ===

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

Additionally, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended.

=== Configure database settings ===

Please be sure to [[Database_configuration|configure important database settings]] prior to installation. While you might be able to use the refbase package without modifying the default settings, we highly recommend not to use the default values.

=== Install refbase via ''install.php'' ===

Point your web browser to ''install.php'', and fill out and submit the install form to complete the installation process.

Note that the install script currently requires a user with full access to the ''mysql'' database (more info [[#Additional_web-install_requirements|below]]). I.e., if you're trying to install refbase on a shared host with limited MySQL access privileges, you may need to perform a [[#Manual_installation|manual installation]] instead.

== Alternative installation methods ==

=== Manual installation ===

If you're experiencing problems with the web-based installation you can try a [[manual installation]] instead.

=== Gentoo Linux ===

[http://www.gentoo.org/ Gentoo] has an [https://packages.gentoo.org/packages/app-text/refbase ebuild of refbase] in [https://wiki.gentoo.org/wiki/Portage portage], so you can merely:

 $ emerge refbase

=== Mandrake/Mandriva Linux ===

[https://pkgs.org/download/refbase refbase RPMs] are available. RPMs for refbase-0.9.5 are available e.g. [ftp://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/devel/cooker/i586/media/contrib/release/refbase-0.9.5-2mdv2010.0.noarch.rpm here]. To install the refbase RPM, use ''urpmi'' or ''rpmdrake'':

 $ urpmi refbase

then finish the installation by pointing your web browser to &lt;code&gt;&lt;nowiki&gt;http://localhost/refbase/install.php&lt;/nowiki&gt;&lt;/code&gt;

== Installation Troubleshooting ==

A list of possible problems and their solutions can be found in the [[Installation-Troubleshooting]] section.

== Installation over an existing database ==

In the install form, you will find a cautionary note:

 Note that, if there's already an existing database with the name specified
 in $databaseName, clicking the Install button will overwrite ALL data in that
 database!

Actually, this note is only true if you're installing into an '''existing refbase database'''. The refbase ''install.php'' script will NOT delete an existing database but will only overwrite those [[MySQL tables|tables]] in the specifed database that have names identical to the ones used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables.

In other words, if the table names in your existing database don't conflict with the table names used by refbase (or if you rename the refbase table names in ''db.inc.php'' AND in ''install.sql'' '''prior to installation''' so that they don't conflict with existing table names), then you should be able to use ''install.php'' for installation of refbase into any existing database.

However, it is a very good idea to make a [[Backup the database|full backup]] of your existing database prior to installation. Also, it may be worth to first do some testing with a non-critical database copy.

== Additional web-install requirements ==

In order to run the ''install.php'' script as described above, you will need a MySQL username with permission to modify the database named ''mysql'' which stores the MySQL [https://dev.mysql.com/doc/refman/8.0/en/privileges-provided.html user privilege] information. This is since the refbase install script adds a dedicated MySQL user to the ''mysql'' database which will be used with your refbase application ([[Add MySQL User|more info]]).

Some shared hosts do not provide MySQL usernames with the required permissions, but instead provide alternate interfaces for MySQL username administration such as a web-based control center. If you face this restriction, you will need to perform a [[#Manual_installation|manual installation]].

[[Category:Installation]]
__NOEDITSECTION__</text>
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  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Updating refbase</title>
  <ns>0</ns>
  <id>20</id>
  <revision>
    <id>66</id>
    <timestamp>2023-10-26T13:55:02Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 31-Oct-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3878" xml:space="preserve">This document describes how to upgrade an existing refbase installation to the most recent version. See the 'UPDATE' file that comes with the refbase package for latest information regarding the update process.

== Backup your database &amp; settings ==

We strongly recommend to [[backup the database|backup]] your existing refbase database before proceeding! You may also want to make a backup copy of your refbase scripts folder. It's especially important that you make a backup copy of the files ''db.inc.php'' and ''ini.inc.php'' (which are located within the ''initialize'' subdirectory of your refbase base directory).

== Download and install scripts ==

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

If you haven't done already, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended. See [[Bibutils#Installing_Bibutils_for_use_with_refbase|here]] for help on how to enable Bibutils for an existing refbase installation.

== Re-apply your database settings ==

Open the new files ''db.inc.php'' and ''ini.inc.php'' and insert again your modifications from the old ''db.inc.php'' and ''ini.inc.php'' files which you backed up in step 1. A good [http://en.wikipedia.org/wiki/Text_editor text editor] (or [http://en.wikipedia.org/wiki/File_comparison file comparison] tool) that is able to compare two versions of the same file can help to solve this task.

== Update MySQL database ==

There are two methods (web-based &amp; manual) to update the refbase MySQL database. The web-based update method uses the ''update.php'' script and is highly recommended since it's update mechanism is generally smarter and more flexible than the manual update method which uses ''update.sql''. In any case, your data should remain untouched by the update operation.

Note that the update process requires a MySQL user that has administrative permissions for the refbase MySQL database, which must include these permissions:

 SELECT, INSERT, UPDATE, DELETE, CREATE, ALTER, DROP, INDEX

=== Web-based update ===

Point your web browser to ''update.php'', supply the user name and password of a MySQL user that has administrative permissions for the refbase MySQL database (see above), and click the "Update" button to complete the update process. A detailed log will be generated for all performed update actions.

=== Manual update ===

If, for some reason, you cannot use the (recommended) web-based update method, you can use the MySQL structure file (''update.sql'') that comes with the refbase package to manually add/alter the MySQL tables that were added/changed in the newest refbase version. To perform the database update, open a command line shell, make your deployment directory the current working directory (&lt;code&gt;cd ...&lt;/code&gt;) and execute the following command:

 mysql -h localhost -uADMINUSER -p --database=DATABASE_NAME &lt; update.sql

where &lt;code&gt;DATABASE_NAME&lt;/code&gt; is the database name that you've specified in variable &lt;code&gt;$databaseName&lt;/code&gt; (in file ''initialize/db.inc.php'') for refbase. &lt;code&gt;ADMINUSER&lt;/code&gt; must be replaced with the name of the MySQL user that has administrative permissions for the refbase MySQL database (see above). You'll be asked for the password of this user to confirm execution of this command.


You should now have a working installation of the most recent refbase version.

[[refbase:Community_Portal|Let us know]], if you run into any problems!

[[Category:Installation]]</text>
    <sha1>fa089fffd1126acd64a59a2241c4a4340a61a224</sha1>
  </revision>
  <revision>
    <id>67</id>
    <parentid>66</parentid>
    <timestamp>2023-10-26T13:55:29Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3896" xml:space="preserve">This document describes how to upgrade an existing refbase installation to the most recent version. See the 'UPDATE' file that comes with the refbase package for latest information regarding the update process.

== Backup your database &amp; settings ==

We strongly recommend to [[backup the database|backup]] your existing refbase database before proceeding! You may also want to make a backup copy of your refbase scripts folder. It's especially important that you make a backup copy of the files ''db.inc.php'' and ''ini.inc.php'' (which are located within the ''initialize'' subdirectory of your refbase base directory).

== Download and install scripts ==

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

If you haven't done already, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended. See [[Bibutils#Installing_Bibutils_for_use_with_refbase|here]] for help on how to enable Bibutils for an existing refbase installation.

== Re-apply your database settings ==

Open the new files ''db.inc.php'' and ''ini.inc.php'' and insert again your modifications from the old ''db.inc.php'' and ''ini.inc.php'' files which you backed up in step 1. A good [http://en.wikipedia.org/wiki/Text_editor text editor] (or [http://en.wikipedia.org/wiki/File_comparison file comparison] tool) that is able to compare two versions of the same file can help to solve this task.

== Update MySQL database ==

There are two methods (web-based &amp; manual) to update the refbase MySQL database. The web-based update method uses the ''update.php'' script and is highly recommended since it's update mechanism is generally smarter and more flexible than the manual update method which uses ''update.sql''. In any case, your data should remain untouched by the update operation.

Note that the update process requires a MySQL user that has administrative permissions for the refbase MySQL database, which must include these permissions:

 SELECT, INSERT, UPDATE, DELETE, CREATE, ALTER, DROP, INDEX

=== Web-based update ===

Point your web browser to ''update.php'', supply the user name and password of a MySQL user that has administrative permissions for the refbase MySQL database (see above), and click the "Update" button to complete the update process. A detailed log will be generated for all performed update actions.

=== Manual update ===

If, for some reason, you cannot use the (recommended) web-based update method, you can use the MySQL structure file (''update.sql'') that comes with the refbase package to manually add/alter the MySQL tables that were added/changed in the newest refbase version. To perform the database update, open a command line shell, make your deployment directory the current working directory (&lt;code&gt;cd ...&lt;/code&gt;) and execute the following command:

 mysql -h localhost -uADMINUSER -p --database=DATABASE_NAME &lt; update.sql

where &lt;code&gt;DATABASE_NAME&lt;/code&gt; is the database name that you've specified in variable &lt;code&gt;$databaseName&lt;/code&gt; (in file ''initialize/db.inc.php'') for refbase. &lt;code&gt;ADMINUSER&lt;/code&gt; must be replaced with the name of the MySQL user that has administrative permissions for the refbase MySQL database (see above). You'll be asked for the password of this user to confirm execution of this command.


You should now have a working installation of the most recent refbase version.

[[refbase:Community_Portal|Let us know]], if you run into any problems!

[[Category:Installation]]
__NOEDITSECTION__</text>
    <sha1>3fdf501eade7345df9c5a51e9a9d9dbfc40e3e23</sha1>
  </revision>
  <revision>
    <id>68</id>
    <parentid>67</parentid>
    <timestamp>2023-10-26T13:58:08Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update link to Community_Portal page</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3896" xml:space="preserve">This document describes how to upgrade an existing refbase installation to the most recent version. See the 'UPDATE' file that comes with the refbase package for latest information regarding the update process.

== Backup your database &amp; settings ==

We strongly recommend to [[backup the database|backup]] your existing refbase database before proceeding! You may also want to make a backup copy of your refbase scripts folder. It's especially important that you make a backup copy of the files ''db.inc.php'' and ''ini.inc.php'' (which are located within the ''initialize'' subdirectory of your refbase base directory).

== Download and install scripts ==

[http://sourceforge.net/project/showfiles.php?group_id=64647 Download] the latest stable release version (or, alternatively, get the latest development version of refbase from the refbase [[SVN_version|SVN repository]]). Then, unpack the download archive (if necessary) and copy all refbase scripts to your server's web directory.

If you haven't done already, you may want to download [[Bibutils]] and copy the binaries to an executable path. Bibutils provides additional import and export funtionality to refbase (e.g. support for Endnote &amp; BibTeX). It is optional, but highly recommended. See [[Bibutils#Installing_Bibutils_for_use_with_refbase|here]] for help on how to enable Bibutils for an existing refbase installation.

== Re-apply your database settings ==

Open the new files ''db.inc.php'' and ''ini.inc.php'' and insert again your modifications from the old ''db.inc.php'' and ''ini.inc.php'' files which you backed up in step 1. A good [http://en.wikipedia.org/wiki/Text_editor text editor] (or [http://en.wikipedia.org/wiki/File_comparison file comparison] tool) that is able to compare two versions of the same file can help to solve this task.

== Update MySQL database ==

There are two methods (web-based &amp; manual) to update the refbase MySQL database. The web-based update method uses the ''update.php'' script and is highly recommended since it's update mechanism is generally smarter and more flexible than the manual update method which uses ''update.sql''. In any case, your data should remain untouched by the update operation.

Note that the update process requires a MySQL user that has administrative permissions for the refbase MySQL database, which must include these permissions:

 SELECT, INSERT, UPDATE, DELETE, CREATE, ALTER, DROP, INDEX

=== Web-based update ===

Point your web browser to ''update.php'', supply the user name and password of a MySQL user that has administrative permissions for the refbase MySQL database (see above), and click the "Update" button to complete the update process. A detailed log will be generated for all performed update actions.

=== Manual update ===

If, for some reason, you cannot use the (recommended) web-based update method, you can use the MySQL structure file (''update.sql'') that comes with the refbase package to manually add/alter the MySQL tables that were added/changed in the newest refbase version. To perform the database update, open a command line shell, make your deployment directory the current working directory (&lt;code&gt;cd ...&lt;/code&gt;) and execute the following command:

 mysql -h localhost -uADMINUSER -p --database=DATABASE_NAME &lt; update.sql

where &lt;code&gt;DATABASE_NAME&lt;/code&gt; is the database name that you've specified in variable &lt;code&gt;$databaseName&lt;/code&gt; (in file ''initialize/db.inc.php'') for refbase. &lt;code&gt;ADMINUSER&lt;/code&gt; must be replaced with the name of the MySQL user that has administrative permissions for the refbase MySQL database (see above). You'll be asked for the password of this user to confirm execution of this command.


You should now have a working installation of the most recent refbase version.

[[refbase:Community_portal|Let us know]], if you run into any problems!

[[Category:Installation]]
__NOEDITSECTION__</text>
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</page>
<page arvcontinue="20231026120622|54">
  <title>MediaWiki:Sitenotice</title>
  <ns>8</ns>
  <id>21</id>
  <revision>
    <id>69</id>
    <timestamp>2023-10-26T14:04:23Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Adds a site notice about the wiki currently being rebuilt</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="94" xml:space="preserve">
Note: This wiki is currently being rebuilt, many pages &amp; links are still outdated or missing.</text>
    <sha1>00f2c514b91a50eca600dd0224c262f679cf4ac2</sha1>
  </revision>
  <revision>
    <id>70</id>
    <parentid>69</parentid>
    <timestamp>2023-10-26T14:08:13Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Center &amp; bolden site notice</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="164" xml:space="preserve">
&lt;div align="center"&gt;
&lt;div id="refbase-site-notice"&gt;'''Note: This wiki is currently being rebuilt, many pages &amp; links are still outdated or missing.'''&lt;/div&gt;
&lt;/div&gt;</text>
    <sha1>470c6972b4f90788080fdfd163e75bfb96dee74e</sha1>
  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>SVN version</title>
  <ns>0</ns>
  <id>22</id>
  <revision>
    <id>71</id>
    <timestamp>2023-10-31T21:20:21Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 19-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2688" xml:space="preserve">== Differences between SVN and release version ==

The refbase SVN ([http://subversion.tigris.org/ Subversion]) version control repository currently has only few changes compared to our release version (refbase-0.9.5), which may be downloaded from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page].

== About refbase SVN ==

Subversion access of refbase is described on [http://sourceforge.net/svn/?group_id=64647 SourceForge].

refbase's [http://refbase.svn.sourceforge.net/viewvc/refbase/ SVN repository] has three root-level directories:

* branches (for bleeding-edge development)
* tags (for releases)
* trunk (which features well-tested changes from the bleeding-edge branch &amp; is newer than any of the tags)

If you are testing or deploying from Subversion, you are encouraged to checkout the trunk:

 svn co https://refbase.svn.sourceforge.net/svnroot/refbase/trunk refbase

If you are a developer who is adding new features to refbase, you are encouraged to check them into the bleeding-edge branch:

 svn co https://refbase.svn.sourceforge.net/svnroot/refbase/branches/bleeding-edge refbase

If checked out from Subversion via one of the above methods, refbase will need no other reorganization third-party PHP files to work. (You may still need to make changes to the database, customize your initialization files, and/or have executables such as [[Bibutils]] installed.)

== Deploying refbase from SVN ==

You can follow the general [[Installing_refbase|installation]] (or [[Updating_refbase|update]]) process, except that you checkout the refbase scripts from SVN. In short, perform following steps to install or update refbase from SVN:

=== Installing refbase from SVN ===

* Checkout the refbase SVN trunk into a local working directory (see above).
* Copy all refbase scripts from your local working directory to your server's web directory.
*[[Database_configuration|Configure]] files ''db.inc.php'' and ''ini.inc.php''.
* Execute ''install.php'' in your browser to install the refbase MySQL database.

=== Updating an existing refbase installation to the SVN version ===

* [[Backup_the_database|Backup]] your existing refbase scripts (especially those in ''initialize/'') as well as your refbase database.
* Checkout the refbase SVN trunk into a local working directory (see above).
* Replace '''all''' your old refbase scripts with the updated ones from the SVN trunk.
* Re-enter your custom settings in files ''db.inc.php'' and ''ini.inc.php''.
* Execute ''update.php'' in your browser to update your refbase MySQL database.


[[refbase:Community_Portal|Let us know]], if you run into any problems!

[[Category:Installation]]</text>
    <sha1>f944ef7f5304a436ac20291602edbc0e38c47a3f</sha1>
  </revision>
  <revision>
    <id>72</id>
    <parentid>71</parentid>
    <timestamp>2023-10-31T21:21:28Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2706" xml:space="preserve">== Differences between SVN and release version ==

The refbase SVN ([http://subversion.tigris.org/ Subversion]) version control repository currently has only few changes compared to our release version (refbase-0.9.5), which may be downloaded from the [http://sourceforge.net/project/showfiles.php?group_id=64647 SourceForge download page].

== About refbase SVN ==

Subversion access of refbase is described on [http://sourceforge.net/svn/?group_id=64647 SourceForge].

refbase's [http://refbase.svn.sourceforge.net/viewvc/refbase/ SVN repository] has three root-level directories:

* branches (for bleeding-edge development)
* tags (for releases)
* trunk (which features well-tested changes from the bleeding-edge branch &amp; is newer than any of the tags)

If you are testing or deploying from Subversion, you are encouraged to checkout the trunk:

 svn co https://refbase.svn.sourceforge.net/svnroot/refbase/trunk refbase

If you are a developer who is adding new features to refbase, you are encouraged to check them into the bleeding-edge branch:

 svn co https://refbase.svn.sourceforge.net/svnroot/refbase/branches/bleeding-edge refbase

If checked out from Subversion via one of the above methods, refbase will need no other reorganization third-party PHP files to work. (You may still need to make changes to the database, customize your initialization files, and/or have executables such as [[Bibutils]] installed.)

== Deploying refbase from SVN ==

You can follow the general [[Installing_refbase|installation]] (or [[Updating_refbase|update]]) process, except that you checkout the refbase scripts from SVN. In short, perform following steps to install or update refbase from SVN:

=== Installing refbase from SVN ===

* Checkout the refbase SVN trunk into a local working directory (see above).
* Copy all refbase scripts from your local working directory to your server's web directory.
*[[Database_configuration|Configure]] files ''db.inc.php'' and ''ini.inc.php''.
* Execute ''install.php'' in your browser to install the refbase MySQL database.

=== Updating an existing refbase installation to the SVN version ===

* [[Backup_the_database|Backup]] your existing refbase scripts (especially those in ''initialize/'') as well as your refbase database.
* Checkout the refbase SVN trunk into a local working directory (see above).
* Replace '''all''' your old refbase scripts with the updated ones from the SVN trunk.
* Re-enter your custom settings in files ''db.inc.php'' and ''ini.inc.php''.
* Execute ''update.php'' in your browser to update your refbase MySQL database.


[[refbase:Community_Portal|Let us know]], if you run into any problems!

[[Category:Installation]]
__NOEDITSECTION__</text>
    <sha1>85d3d9f865d0819bce94aa06ff1de5cfbe4782ab</sha1>
  </revision>
  <revision>
    <id>73</id>
    <parentid>72</parentid>
    <timestamp>2023-10-31T21:46:55Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update links and text</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2750" xml:space="preserve">== Differences between SVN and release version ==

Compared to the latest release version, which may be downloaded from the [https://sourceforge.net/projects/refbase/files/ SourceForge download page], the refbase SVN ([https://subversion.apache.org/ Subversion]) version control repository currently mostly contains changes related to PHP &amp; MySQL compatibility.

== About refbase SVN ==

refbase's [https://sourceforge.net/p/refbase/code/ SVN repository] has three root-level directories:

* branches (for bleeding-edge development)
* tags (for releases)
* trunk (which features well-tested changes from the bleeding-edge branch &amp; is newer than any of the tags)

If you are testing or deploying from Subversion, you are encouraged to checkout the trunk:

 svn checkout https://svn.code.sf.net/p/refbase/code/trunk refbase

If you are a developer who is adding new features to refbase, you are encouraged to check them into the bleeding-edge branch:

 svn checkout https://svn.code.sf.net/p/refbase/code/branches/bleeding-edge refbase

If checked out from Subversion via one of the above methods, refbase will need no other reorganization third-party PHP files to work. (You may still need to make changes to the database, customize your initialization files, and/or have executables such as [[Bibutils]] installed.)

== Deploying refbase from SVN ==

You can follow the general [[Installing_refbase|installation]] (or [[Updating_refbase|update]]) process, except that you checkout the refbase scripts from SVN. In short, perform following steps to install or update refbase from SVN:

=== Installing refbase from SVN ===

* Checkout the refbase SVN trunk into a local working directory (see above).
* Copy all refbase scripts from your local working directory to your server's web directory.
*[[Database_configuration|Configure]] files ''db.inc.php'' and ''ini.inc.php''.
* Execute ''install.php'' in your browser to install the refbase MySQL database.
* Remove ''install.php'' &amp; ''update.php'' from your server's web directory.

=== Updating an existing refbase installation to the SVN version ===

* [[Backup_the_database|Backup]] your existing refbase scripts (especially those in ''initialize/'') as well as your refbase database.
* Checkout the refbase SVN trunk into a local working directory (see above).
* Replace '''all''' your old refbase scripts with the updated ones from the SVN trunk.
* Re-enter your custom settings in files ''db.inc.php'' and ''ini.inc.php''.
* Execute ''update.php'' in your browser to update your refbase MySQL database.
* Remove ''install.php'' &amp; ''update.php'' from your server's web directory.


[[refbase:Community_Portal|Let us know]], if you run into any problems!

[[Category:Installation]]
__NOEDITSECTION__</text>
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<page arvcontinue="20231026120622|54">
  <title>Requirements</title>
  <ns>0</ns>
  <id>23</id>
  <revision>
    <id>75</id>
    <timestamp>2023-11-05T17:20:26Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 31-Oct-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1600" xml:space="preserve">Installation of the refbase package requires:

* the refbase scripts ([http://sourceforge.net/project/showfiles.php?group_id=64647 official release] or latest [[SVN version|development version]] from SVN)
* a web server (like the [http://httpd.apache.org/ Apache HTTP Server])
* [http://www.php.net/ PHP] (version 4.4.0 or greater) with enabled session support &amp; installed PHP MySQL module
* [http://www.mysql.com/ MySQL] (version 4.1.x or greater required for Unicode support)
** the [http://www.xampp.org/ Apache Friends] project offers a complete solution for above mentioned services (Apache, PHP, MySQL), called XAMPP; the easy-to-use package is available for different platforms (Linux, Windows, Mac OS X, Solaris) 
* optionally, [[Bibutils]] for import and export of various formats (e.g., Endnote &amp; BibTeX)

In addition, there are some [[Required PHP-INI Settings|required ''php.ini'' settings]].

refbase-0.9.0 or greater has these further requirements:

* the features that allow for automatic renaming of uploaded files require the [http://www.php.net/manual/en/ref.iconv.php iconv functions], i.e. PHP must have been compiled with the &lt;code&gt;--with-iconv&lt;/code&gt; configure-option
* Unicode (UTF-8) support requires the [http://de3.php.net/manual/en/ref.mbstring.php multibyte string functions] being enabled on your PHP server, i.e., PHP must have been compiled with the &lt;code&gt;--enable-mbstring&lt;/code&gt; configure option; however, refbase can be used with a latin1 (ISO-8859-1) database if multibyte support is not available on your server

[[Category:Installation]]
[[Category:Requirements]]</text>
    <sha1>b2d2e12129a4cb3c21e49a185df04b812092c23e</sha1>
  </revision>
  <revision>
    <id>76</id>
    <parentid>75</parentid>
    <timestamp>2023-11-05T17:27:02Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1609" xml:space="preserve">Installation of the refbase package requires:

* the refbase scripts ([http://sourceforge.net/project/showfiles.php?group_id=64647 official release] or latest [[SVN version|development version]] from SVN)
* a web server (like the [http://httpd.apache.org/ Apache HTTP Server])
* [http://www.php.net/ PHP] (version 4.4.0 or greater) with enabled session support &amp; installed PHP MySQL module
* [http://www.mysql.com/ MySQL] (version 4.1.x or greater required for Unicode support)
** the [https://www.apachefriends.org Apache Friends] project offers a complete solution for above mentioned services (Apache, PHP, MySQL), called XAMPP; the easy-to-use package is available for different platforms (Linux, Windows, Mac OS X, Solaris) 
* optionally, [[Bibutils]] for import and export of various formats (e.g., Endnote &amp; BibTeX)

In addition, there are some [[Required PHP-INI Settings|required ''php.ini'' settings]].

refbase-0.9.0 or greater has these further requirements:

* the features that allow for automatic renaming of uploaded files require the [http://www.php.net/manual/en/ref.iconv.php iconv functions], i.e. PHP must have been compiled with the &lt;code&gt;--with-iconv&lt;/code&gt; configure-option
* Unicode (UTF-8) support requires the [https://www.php.net/manual/en/ref.mbstring.php multibyte string functions] being enabled on your PHP server, i.e., PHP must have been compiled with the &lt;code&gt;--enable-mbstring&lt;/code&gt; configure option; however, refbase can be used with a latin1 (ISO-8859-1) database if multibyte support is not available on your server

[[Category:Installation]]
[[Category:Requirements]]</text>
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<page arvcontinue="20231026120622|54">
  <title>Required PHP-INI Settings</title>
  <ns>0</ns>
  <id>24</id>
  <revision>
    <id>77</id>
    <timestamp>2023-11-05T17:29:13Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 31-Oct-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2109" xml:space="preserve">The refbase PHP scripts will only work correctly if the following settings are present within your PHP configuration file (''php.ini''):

&lt;table border="0"&gt;

&lt;tr&gt;&lt;th align="left" width="170"&gt;Directive&lt;/th&gt;&lt;th align="left" width="70"&gt;Value&lt;/th&gt;&lt;th align="left"&gt;Notes&lt;/th&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;session.use_cookies&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;file_uploads&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;allow_url_fopen&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;(only required for the "Import IDs" feature, e.g. import from PMID or DOI)&lt;/td&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;magic_quotes_gpc&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;(only necessary for versions prior to refbase-0.9.0)&lt;/td&gt;&lt;/tr&gt;

&lt;/table&gt;
("1" is equivalent to "On")

Note that export to BibTeX, Endote or RIS (via [[Bibutils]]) uses the &lt;code&gt;exec()&lt;/code&gt; function. I.e., if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in ''php.ini'' then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;.

Additionally, be sure you've set the values for the directives &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; to be large enough to handle your uploads. If you're experiencing script execution timeouts, you may want to increase the values for &lt;code&gt;max_execution_time&lt;/code&gt;, &lt;code&gt;max_input_time&lt;/code&gt; and &lt;code&gt;memory_limit&lt;/code&gt;. As a general rule, &lt;code&gt;memory_limit&lt;/code&gt; should be substantially greater than &lt;code&gt;post_max_size&lt;/code&gt; which, in turn, should be greater than &lt;code&gt;upload_max_filesize&lt;/code&gt;.

You'll need to restart your web server to apply any changes you've made.

== How to locate your active ''php.ini'' file ==

Check your PHP documentation for the location of the ''php.ini'' file. Its location depends on the platform and PHP version you're using. Alternatively, you can call the &lt;code&gt;phpinfo()&lt;/code&gt; function which will tell you the location of this file. To call this function, simply put the string

 &lt;?php phpinfo() ?&gt;

into a ''.php'' file within your web directory and access this file via your browser.

[[Category:Installation]]
[[Category:Requirements]]</text>
    <sha1>5e2c2135fb8d198c6fbbfcef6b0283d2bd0a55ea</sha1>
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  <revision>
    <id>78</id>
    <parentid>77</parentid>
    <timestamp>2023-11-05T17:38:22Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2127" xml:space="preserve">The refbase PHP scripts will only work correctly if the following settings are present within your PHP configuration file (''php.ini''):

&lt;table border="0"&gt;

&lt;tr&gt;&lt;th align="left" width="170"&gt;Directive&lt;/th&gt;&lt;th align="left" width="70"&gt;Value&lt;/th&gt;&lt;th align="left"&gt;Notes&lt;/th&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;session.use_cookies&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;file_uploads&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;&lt;/td&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;allow_url_fopen&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;(only required for the "Import IDs" feature, e.g. import from PMID or DOI)&lt;/td&gt;&lt;/tr&gt;

&lt;tr&gt;&lt;td&gt;&lt;code&gt;magic_quotes_gpc&lt;/code&gt;&lt;/td&gt;&lt;td&gt;On&lt;/td&gt;&lt;td&gt;(only necessary for versions prior to refbase-0.9.0)&lt;/td&gt;&lt;/tr&gt;

&lt;/table&gt;
("1" is equivalent to "On")

Note that export to BibTeX, Endote or RIS (via [[Bibutils]]) uses the &lt;code&gt;exec()&lt;/code&gt; function. I.e., if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in ''php.ini'' then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;.

Additionally, be sure you've set the values for the directives &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; to be large enough to handle your uploads. If you're experiencing script execution timeouts, you may want to increase the values for &lt;code&gt;max_execution_time&lt;/code&gt;, &lt;code&gt;max_input_time&lt;/code&gt; and &lt;code&gt;memory_limit&lt;/code&gt;. As a general rule, &lt;code&gt;memory_limit&lt;/code&gt; should be substantially greater than &lt;code&gt;post_max_size&lt;/code&gt; which, in turn, should be greater than &lt;code&gt;upload_max_filesize&lt;/code&gt;.

You'll need to restart your web server to apply any changes you've made.

== How to locate your active ''php.ini'' file ==

Check your PHP documentation for the location of the ''php.ini'' file. Its location depends on the platform and PHP version you're using. Alternatively, you can call the &lt;code&gt;phpinfo()&lt;/code&gt; function which will tell you the location of this file. To call this function, simply put the string

 &lt;?php phpinfo() ?&gt;

into a ''.php'' file within your web directory and access this file via your browser.

[[Category:Installation]]
[[Category:Requirements]]
__NOEDITSECTION__</text>
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</page>
<page arvcontinue="20231026120622|54">
  <title>Bibutils</title>
  <ns>0</ns>
  <id>25</id>
  <revision>
    <id>79</id>
    <timestamp>2023-11-05T17:41:29Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 23-Jan-2009</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4674" xml:space="preserve">This page describes the refbase integration with Bibutils.

== About Bibutils ==

[http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

* BibTeX -&gt; MODS XML (&lt;code&gt;bib2xml&lt;/code&gt;)
* Copac -&gt; MODS XML (&lt;code&gt;copac2xml&lt;/code&gt;)
* Endnote (Refer format) -&gt; MODS XML (&lt;code&gt;end2xml&lt;/code&gt;)
* Endnote (Endnote XML format) -&gt; MODS XML (&lt;code&gt;endx2xml&lt;/code&gt;)
* ISI Web of Science -&gt; MODS XML (&lt;code&gt;isi2xml&lt;/code&gt;)
* Pubmed XML -&gt; MODS XML (&lt;code&gt;med2xml&lt;/code&gt;)
* RIS -&gt; MODS XML (&lt;code&gt;ris2xml&lt;/code&gt;)

* MODS XML -&gt; ADS (&lt;code&gt;xml2ads&lt;/code&gt;)
* MODS XML -&gt; BibTeX (&lt;code&gt;xml2bib&lt;/code&gt;)
* MODS XML -&gt; Endnote (&lt;code&gt;xml2end&lt;/code&gt;)
* MODS XML -&gt; ISI Web of Science (&lt;code&gt;xml2isi&lt;/code&gt;)
* MODS XML -&gt; Reference Manager/RIS (&lt;code&gt;xml2ris&lt;/code&gt;)
* MODS XML -&gt; Word 2007 XML Bibliography format (&lt;code&gt;xml2wordbib&lt;/code&gt;)

Bibutils is available for various platforms and can be downloaded as binaries or source code from the [http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils home page] or the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be installed via platform-specific package management systems:

* [http://gentoo-portage.com/app-text/bibutils Gentoo Linux]
* [http://club.mandriva.com/xwiki/bin/view/KB/Bibutils Mandriva Linux]
* [http://www.macports.org/ports.php?by=name&amp;substr=bibutils MacPorts]

== refbase integration with Bibutils ==

refbase-0.9.0 and above requires Bibutils (version 3.21 or greater) for following formats:

* import:
** BibTeX
** Copac
** Endnote (Refer format)
** Endnote (Endnote XML format)
** PubMed XML
** MODS XML

* export:
** ADS
** BibTeX
** Endnote
** ISI Web of Science
** Reference Manager/RIS
** Word 2007 XML Bibliography format

I.e., to [[Importing records|import]] or [[Exporting records|export]] any of the above listed formats, you'll need to install Bibutils on your server.

=== Installing Bibutils for use with refbase ===

In general, you can install the Bibutils programs wherever you like, but they must be executable by your server, i.e. they must be located within an executable path and the Bibutils programs itself must be executable. However, if the &lt;code&gt;safe_mode&lt;/code&gt; setting in your active ''php.ini'' file is set to On, then you'll need to put the Bibutils programs within the directory that's specified in the &lt;code&gt;safe_mode_exec_dir&lt;/code&gt; setting. Information on how to locate your active ''php.ini'' file is given [[Required PHP-INI Settings|here]]. Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x---), and the Bibutils programs should have permissions 755 (rwxr-xr-x).

Once you've installed Bibutils on your server, the path to the Bibutils programs must be set accordingly in the refbase MySQL table ''depends''. The easiest way to setup refbase with Bibutils is to do so upon installation using the provided ''install.php'' script. The ''install.php'' script will attempt to locate Bibutils for you if it is installed on your server.

A method to ensure that the install script locates Bibutils when your Bibutils is installed to a non-standard path is to symlink your Bibutils path into the directory containing ''install.php'' with the name "bibutils".  This approach requires that your web server is configured to follow symlinks.  

 % ln -s /path/to/bibutils /path/to/refbase/bibutils

Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, you can set the path to Bibutils directly by issuing following MySQL command via a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or from within your MySQL command line interpreter:

 UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";

Note that, in the above command, you must replace &lt;code&gt;/path/to/bibutils/&lt;/code&gt; with the actual (full) directory path to your Bibutils programs. On Windows, you probably need to use backslashes as path separators (&lt;code&gt;\path\to\bibutils\&lt;/code&gt;). Also note that the given path must end with a slash.

Finally, when setting up Bibutils for an existing refbase installation, please make sure that Bibutils is properly enabled for refbase by issuing following MySQL command:

 UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

[[refbase:Community_Portal|Let us know]] if you run into problems.

[[Category:Installation]]
[[Category:Requirements]]</text>
    <sha1>eb77f7adcd31871533cfd69559db2bda3f66f306</sha1>
  </revision>
  <revision>
    <id>80</id>
    <parentid>79</parentid>
    <timestamp>2023-11-05T17:42:04Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4692" xml:space="preserve">This page describes the refbase integration with Bibutils.

== About Bibutils ==

[http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

* BibTeX -&gt; MODS XML (&lt;code&gt;bib2xml&lt;/code&gt;)
* Copac -&gt; MODS XML (&lt;code&gt;copac2xml&lt;/code&gt;)
* Endnote (Refer format) -&gt; MODS XML (&lt;code&gt;end2xml&lt;/code&gt;)
* Endnote (Endnote XML format) -&gt; MODS XML (&lt;code&gt;endx2xml&lt;/code&gt;)
* ISI Web of Science -&gt; MODS XML (&lt;code&gt;isi2xml&lt;/code&gt;)
* Pubmed XML -&gt; MODS XML (&lt;code&gt;med2xml&lt;/code&gt;)
* RIS -&gt; MODS XML (&lt;code&gt;ris2xml&lt;/code&gt;)

* MODS XML -&gt; ADS (&lt;code&gt;xml2ads&lt;/code&gt;)
* MODS XML -&gt; BibTeX (&lt;code&gt;xml2bib&lt;/code&gt;)
* MODS XML -&gt; Endnote (&lt;code&gt;xml2end&lt;/code&gt;)
* MODS XML -&gt; ISI Web of Science (&lt;code&gt;xml2isi&lt;/code&gt;)
* MODS XML -&gt; Reference Manager/RIS (&lt;code&gt;xml2ris&lt;/code&gt;)
* MODS XML -&gt; Word 2007 XML Bibliography format (&lt;code&gt;xml2wordbib&lt;/code&gt;)

Bibutils is available for various platforms and can be downloaded as binaries or source code from the [http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils home page] or the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be installed via platform-specific package management systems:

* [http://gentoo-portage.com/app-text/bibutils Gentoo Linux]
* [http://club.mandriva.com/xwiki/bin/view/KB/Bibutils Mandriva Linux]
* [http://www.macports.org/ports.php?by=name&amp;substr=bibutils MacPorts]

== refbase integration with Bibutils ==

refbase-0.9.0 and above requires Bibutils (version 3.21 or greater) for following formats:

* import:
** BibTeX
** Copac
** Endnote (Refer format)
** Endnote (Endnote XML format)
** PubMed XML
** MODS XML

* export:
** ADS
** BibTeX
** Endnote
** ISI Web of Science
** Reference Manager/RIS
** Word 2007 XML Bibliography format

I.e., to [[Importing records|import]] or [[Exporting records|export]] any of the above listed formats, you'll need to install Bibutils on your server.

=== Installing Bibutils for use with refbase ===

In general, you can install the Bibutils programs wherever you like, but they must be executable by your server, i.e. they must be located within an executable path and the Bibutils programs itself must be executable. However, if the &lt;code&gt;safe_mode&lt;/code&gt; setting in your active ''php.ini'' file is set to On, then you'll need to put the Bibutils programs within the directory that's specified in the &lt;code&gt;safe_mode_exec_dir&lt;/code&gt; setting. Information on how to locate your active ''php.ini'' file is given [[Required PHP-INI Settings|here]]. Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x---), and the Bibutils programs should have permissions 755 (rwxr-xr-x).

Once you've installed Bibutils on your server, the path to the Bibutils programs must be set accordingly in the refbase MySQL table ''depends''. The easiest way to setup refbase with Bibutils is to do so upon installation using the provided ''install.php'' script. The ''install.php'' script will attempt to locate Bibutils for you if it is installed on your server.

A method to ensure that the install script locates Bibutils when your Bibutils is installed to a non-standard path is to symlink your Bibutils path into the directory containing ''install.php'' with the name "bibutils".  This approach requires that your web server is configured to follow symlinks.  

 % ln -s /path/to/bibutils /path/to/refbase/bibutils

Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, you can set the path to Bibutils directly by issuing following MySQL command via a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or from within your MySQL command line interpreter:

 UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";

Note that, in the above command, you must replace &lt;code&gt;/path/to/bibutils/&lt;/code&gt; with the actual (full) directory path to your Bibutils programs. On Windows, you probably need to use backslashes as path separators (&lt;code&gt;\path\to\bibutils\&lt;/code&gt;). Also note that the given path must end with a slash.

Finally, when setting up Bibutils for an existing refbase installation, please make sure that Bibutils is properly enabled for refbase by issuing following MySQL command:

 UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

[[refbase:Community_Portal|Let us know]] if you run into problems.

[[Category:Installation]]
[[Category:Requirements]]
__NOEDITSECTION__</text>
    <sha1>982e7d6db8bdc99a3ee556e4f11ba6595590b6a0</sha1>
  </revision>
  <revision>
    <id>81</id>
    <parentid>80</parentid>
    <timestamp>2023-11-05T17:53:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update link to Community_portal page</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4692" xml:space="preserve">This page describes the refbase integration with Bibutils.

== About Bibutils ==

[http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

* BibTeX -&gt; MODS XML (&lt;code&gt;bib2xml&lt;/code&gt;)
* Copac -&gt; MODS XML (&lt;code&gt;copac2xml&lt;/code&gt;)
* Endnote (Refer format) -&gt; MODS XML (&lt;code&gt;end2xml&lt;/code&gt;)
* Endnote (Endnote XML format) -&gt; MODS XML (&lt;code&gt;endx2xml&lt;/code&gt;)
* ISI Web of Science -&gt; MODS XML (&lt;code&gt;isi2xml&lt;/code&gt;)
* Pubmed XML -&gt; MODS XML (&lt;code&gt;med2xml&lt;/code&gt;)
* RIS -&gt; MODS XML (&lt;code&gt;ris2xml&lt;/code&gt;)

* MODS XML -&gt; ADS (&lt;code&gt;xml2ads&lt;/code&gt;)
* MODS XML -&gt; BibTeX (&lt;code&gt;xml2bib&lt;/code&gt;)
* MODS XML -&gt; Endnote (&lt;code&gt;xml2end&lt;/code&gt;)
* MODS XML -&gt; ISI Web of Science (&lt;code&gt;xml2isi&lt;/code&gt;)
* MODS XML -&gt; Reference Manager/RIS (&lt;code&gt;xml2ris&lt;/code&gt;)
* MODS XML -&gt; Word 2007 XML Bibliography format (&lt;code&gt;xml2wordbib&lt;/code&gt;)

Bibutils is available for various platforms and can be downloaded as binaries or source code from the [http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils home page] or the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be installed via platform-specific package management systems:

* [http://gentoo-portage.com/app-text/bibutils Gentoo Linux]
* [http://club.mandriva.com/xwiki/bin/view/KB/Bibutils Mandriva Linux]
* [http://www.macports.org/ports.php?by=name&amp;substr=bibutils MacPorts]

== refbase integration with Bibutils ==

refbase-0.9.0 and above requires Bibutils (version 3.21 or greater) for following formats:

* import:
** BibTeX
** Copac
** Endnote (Refer format)
** Endnote (Endnote XML format)
** PubMed XML
** MODS XML

* export:
** ADS
** BibTeX
** Endnote
** ISI Web of Science
** Reference Manager/RIS
** Word 2007 XML Bibliography format

I.e., to [[Importing records|import]] or [[Exporting records|export]] any of the above listed formats, you'll need to install Bibutils on your server.

=== Installing Bibutils for use with refbase ===

In general, you can install the Bibutils programs wherever you like, but they must be executable by your server, i.e. they must be located within an executable path and the Bibutils programs itself must be executable. However, if the &lt;code&gt;safe_mode&lt;/code&gt; setting in your active ''php.ini'' file is set to On, then you'll need to put the Bibutils programs within the directory that's specified in the &lt;code&gt;safe_mode_exec_dir&lt;/code&gt; setting. Information on how to locate your active ''php.ini'' file is given [[Required PHP-INI Settings|here]]. Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x---), and the Bibutils programs should have permissions 755 (rwxr-xr-x).

Once you've installed Bibutils on your server, the path to the Bibutils programs must be set accordingly in the refbase MySQL table ''depends''. The easiest way to setup refbase with Bibutils is to do so upon installation using the provided ''install.php'' script. The ''install.php'' script will attempt to locate Bibutils for you if it is installed on your server.

A method to ensure that the install script locates Bibutils when your Bibutils is installed to a non-standard path is to symlink your Bibutils path into the directory containing ''install.php'' with the name "bibutils".  This approach requires that your web server is configured to follow symlinks.  

 % ln -s /path/to/bibutils /path/to/refbase/bibutils

Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, you can set the path to Bibutils directly by issuing following MySQL command via a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or from within your MySQL command line interpreter:

 UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";

Note that, in the above command, you must replace &lt;code&gt;/path/to/bibutils/&lt;/code&gt; with the actual (full) directory path to your Bibutils programs. On Windows, you probably need to use backslashes as path separators (&lt;code&gt;\path\to\bibutils\&lt;/code&gt;). Also note that the given path must end with a slash.

Finally, when setting up Bibutils for an existing refbase installation, please make sure that Bibutils is properly enabled for refbase by issuing following MySQL command:

 UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

[[refbase:Community_portal|Let us know]] if you run into problems.

[[Category:Installation]]
[[Category:Requirements]]
__NOEDITSECTION__</text>
    <sha1>1d81a6dccef11317db84b3b150257977a8fe92ea</sha1>
  </revision>
  <revision>
    <id>85</id>
    <parentid>81</parentid>
    <timestamp>2023-11-05T20:09:43Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4794" xml:space="preserve">This page describes the refbase integration with Bibutils.

== About Bibutils ==

[https://sourceforge.net/p/bibutils/home/Bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

* BibTeX -&gt; MODS XML (&lt;code&gt;bib2xml&lt;/code&gt;)
* Copac -&gt; MODS XML (&lt;code&gt;copac2xml&lt;/code&gt;)
* Endnote (Refer format) -&gt; MODS XML (&lt;code&gt;end2xml&lt;/code&gt;)
* Endnote (Endnote XML format) -&gt; MODS XML (&lt;code&gt;endx2xml&lt;/code&gt;)
* ISI Web of Science -&gt; MODS XML (&lt;code&gt;isi2xml&lt;/code&gt;)
* Pubmed XML -&gt; MODS XML (&lt;code&gt;med2xml&lt;/code&gt;)
* RIS -&gt; MODS XML (&lt;code&gt;ris2xml&lt;/code&gt;)


* MODS XML -&gt; ADS (&lt;code&gt;xml2ads&lt;/code&gt;)
* MODS XML -&gt; BibTeX (&lt;code&gt;xml2bib&lt;/code&gt;)
* MODS XML -&gt; Endnote (&lt;code&gt;xml2end&lt;/code&gt;)
* MODS XML -&gt; ISI Web of Science (&lt;code&gt;xml2isi&lt;/code&gt;)
* MODS XML -&gt; Reference Manager/RIS (&lt;code&gt;xml2ris&lt;/code&gt;)
* MODS XML -&gt; Word 2007 XML Bibliography format (&lt;code&gt;xml2wordbib&lt;/code&gt;)

Bibutils is available for various platforms and can be downloaded as source code from the [https://sourceforge.net/projects/bibutils/files/ Bibutils home page] or. Older Bibutils versions are available as binaries from the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be downloaded for various [https://pkgs.org/download/bibutils Linux distributions] or installed via platform-specific package management systems:

* [https://packages.gentoo.org/packages/app-text/bibutils Gentoo Linux]
* [https://formulae.brew.sh/formula/bibutils Homebrew]
* [https://ports.macports.org/port/bibutils/ MacPorts]

== refbase integration with Bibutils ==

refbase-0.9.0 and above requires Bibutils (version 3.21 or greater) for following formats:

* import:
** BibTeX
** Copac
** Endnote (Refer format)
** Endnote (Endnote XML format)
** PubMed XML
** MODS XML

* export:
** ADS
** BibTeX
** Endnote
** ISI Web of Science
** Reference Manager/RIS
** Word 2007 XML Bibliography format

I.e., to [[Importing records|import]] or [[Exporting records|export]] any of the above listed formats, you'll need to install Bibutils on your server.

=== Installing Bibutils for use with refbase ===

In general, you can install the Bibutils programs wherever you like, but they must be executable by your server, i.e. they must be located within an executable path and the Bibutils programs itself must be executable. However, if the &lt;code&gt;safe_mode&lt;/code&gt; setting in your active ''php.ini'' file is set to On, then you'll need to put the Bibutils programs within the directory that's specified in the &lt;code&gt;safe_mode_exec_dir&lt;/code&gt; setting. Information on how to locate your active ''php.ini'' file is given [[Required PHP-INI Settings|here]]. Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x---), and the Bibutils programs should have permissions 755 (rwxr-xr-x).

Once you've installed Bibutils on your server, the path to the Bibutils programs must be set accordingly in the refbase MySQL table ''depends''. The easiest way to setup refbase with Bibutils is to do so upon installation using the provided ''install.php'' script. The ''install.php'' script will attempt to locate Bibutils for you if it is installed on your server.

A method to ensure that the install script locates Bibutils when your Bibutils is installed to a non-standard path is to symlink your Bibutils path into the directory containing ''install.php'' with the name "bibutils".  This approach requires that your web server is configured to follow symlinks.  

 % ln -s /path/to/bibutils /path/to/refbase/bibutils

Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, you can set the path to Bibutils directly by issuing following MySQL command via a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or from within your MySQL command line interpreter:

 UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";

Note that, in the above command, you must replace &lt;code&gt;/path/to/bibutils/&lt;/code&gt; with the actual (full) directory path to your Bibutils programs. On Windows, you probably need to use backslashes as path separators (&lt;code&gt;\path\to\bibutils\&lt;/code&gt;). Also note that the given path must end with a slash.

Finally, when setting up Bibutils for an existing refbase installation, please make sure that Bibutils is properly enabled for refbase by issuing following MySQL command:

 UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

[[refbase:Community_portal|Let us know]] if you run into problems.

[[Category:Installation]]
[[Category:Requirements]]
__NOEDITSECTION__</text>
    <sha1>c95a4f0c4798e45dd3a80cda8f478512ca1bef5d</sha1>
  </revision>
  <revision>
    <id>86</id>
    <parentid>85</parentid>
    <timestamp>2023-11-05T20:16:15Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Group list of Bibutils conversions</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4838" xml:space="preserve">This page describes the refbase integration with Bibutils.

== About Bibutils ==

[https://sourceforge.net/p/bibutils/home/Bibutils/ Bibutils] (bibliography conversion utilities) is a set of command line utilities which interconvert between various bibliography formats using a common XML intermediate called [http://www.loc.gov/standards/mods/ MODS]. Bibutils currently supports following conversions:

* to MODS XML:
** BibTeX -&gt; MODS XML (&lt;code&gt;bib2xml&lt;/code&gt;)
** Copac -&gt; MODS XML (&lt;code&gt;copac2xml&lt;/code&gt;)
** Endnote (Refer format) -&gt; MODS XML (&lt;code&gt;end2xml&lt;/code&gt;)
** Endnote (Endnote XML format) -&gt; MODS XML (&lt;code&gt;endx2xml&lt;/code&gt;)
** ISI Web of Science -&gt; MODS XML (&lt;code&gt;isi2xml&lt;/code&gt;)
** Pubmed XML -&gt; MODS XML (&lt;code&gt;med2xml&lt;/code&gt;)
** RIS -&gt; MODS XML (&lt;code&gt;ris2xml&lt;/code&gt;)

* from MODS XML:
** MODS XML -&gt; ADS (&lt;code&gt;xml2ads&lt;/code&gt;)
** MODS XML -&gt; BibTeX (&lt;code&gt;xml2bib&lt;/code&gt;)
** MODS XML -&gt; Endnote (&lt;code&gt;xml2end&lt;/code&gt;)
** MODS XML -&gt; ISI Web of Science (&lt;code&gt;xml2isi&lt;/code&gt;)
** MODS XML -&gt; Reference Manager/RIS (&lt;code&gt;xml2ris&lt;/code&gt;)
** MODS XML -&gt; Word 2007 XML Bibliography format (&lt;code&gt;xml2wordbib&lt;/code&gt;)

Bibutils is available for various platforms and can be downloaded as source code from the [https://sourceforge.net/projects/bibutils/files/ Bibutils home page] or. Older Bibutils versions are available as binaries from the [http://bibutils.refbase.org/ Bibutils mirror site]. Bibutils can also be downloaded for various [https://pkgs.org/download/bibutils Linux distributions] or installed via platform-specific package management systems:

* [https://packages.gentoo.org/packages/app-text/bibutils Gentoo Linux]
* [https://formulae.brew.sh/formula/bibutils Homebrew]
* [https://ports.macports.org/port/bibutils/ MacPorts]

== refbase integration with Bibutils ==

refbase-0.9.0 and above requires Bibutils (version 3.21 or greater) for following formats:

* import:
** BibTeX
** Copac
** Endnote (Refer format)
** Endnote (Endnote XML format)
** PubMed XML
** MODS XML

* export:
** ADS
** BibTeX
** Endnote
** ISI Web of Science
** Reference Manager/RIS
** Word 2007 XML Bibliography format

I.e., to [[Importing records|import]] or [[Exporting records|export]] any of the above listed formats, you'll need to install Bibutils on your server.

=== Installing Bibutils for use with refbase ===

In general, you can install the Bibutils programs wherever you like, but they must be executable by your server, i.e. they must be located within an executable path and the Bibutils programs itself must be executable. However, if the &lt;code&gt;safe_mode&lt;/code&gt; setting in your active ''php.ini'' file is set to On, then you'll need to put the Bibutils programs within the directory that's specified in the &lt;code&gt;safe_mode_exec_dir&lt;/code&gt; setting. Information on how to locate your active ''php.ini'' file is given [[Required PHP-INI Settings|here]]. Usually, the directory that contains the Bibutils programs should have permission 750 (rwxr-x---), and the Bibutils programs should have permissions 755 (rwxr-xr-x).

Once you've installed Bibutils on your server, the path to the Bibutils programs must be set accordingly in the refbase MySQL table ''depends''. The easiest way to setup refbase with Bibutils is to do so upon installation using the provided ''install.php'' script. The ''install.php'' script will attempt to locate Bibutils for you if it is installed on your server.

A method to ensure that the install script locates Bibutils when your Bibutils is installed to a non-standard path is to symlink your Bibutils path into the directory containing ''install.php'' with the name "bibutils".  This approach requires that your web server is configured to follow symlinks.  

 % ln -s /path/to/bibutils /path/to/refbase/bibutils

Alternatively, if you'd like to enable Bibutils support for an existing refbase installation, you can set the path to Bibutils directly by issuing following MySQL command via a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or from within your MySQL command line interpreter:

 UPDATE depends SET depends_path = "/path/to/bibutils/" WHERE depends_external = "bibutils";

Note that, in the above command, you must replace &lt;code&gt;/path/to/bibutils/&lt;/code&gt; with the actual (full) directory path to your Bibutils programs. On Windows, you probably need to use backslashes as path separators (&lt;code&gt;\path\to\bibutils\&lt;/code&gt;). Also note that the given path must end with a slash.

Finally, when setting up Bibutils for an existing refbase installation, please make sure that Bibutils is properly enabled for refbase by issuing following MySQL command:

 UPDATE depends SET depends_enabled = "true" WHERE depends_external = "bibutils";

[[refbase:Community_portal|Let us know]] if you run into problems.

[[Category:Installation]]
[[Category:Requirements]]
__NOEDITSECTION__</text>
    <sha1>ffa3ab7d695c54697eb543c2dfaa10288d0937af</sha1>
  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Database configuration</title>
  <ns>0</ns>
  <id>26</id>
  <revision>
    <id>87</id>
    <timestamp>2023-11-05T20:22:45Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 31-Oct-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1478" xml:space="preserve">In order to properly configure your database you need to edit some of the configuration files:

* open the file ''initialize/db.inc.php'' in a text editor and edit the values of the following variables:
** &lt;code&gt;$databaseName&lt;/code&gt; must contain the name of your MySQL database (example: "literature")
** &lt;code&gt;$username&lt;/code&gt; must contain the name of the MySQL user that's used with your MySQL database (example: "litwww")
** &lt;code&gt;$password&lt;/code&gt; must contain the password that's required to access your MySQL database (example: "%l1t3ratur3?")
* similarly, open the file ''initialize/ini.inc.php'' and edit all values of the contained variables to fit your needs (please see the comments within the file for further guidance)

Note that the refbase ''install.php'' script adds a new MySQL user to the MySQL database which is appropriate for use with the refbase application ([[Add MySQL User|more info]]).

== Shared database ==

If you are not able to create a new database for your refbase install, you must check that any existing database you configure does not contain tables whose names conflict with the [[MySQL tables]] used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables. See [[Installing refbase#Installation over an existing database|Installation over an existing database]] for more info.

[[Category:Installation]]</text>
    <sha1>c1b12fa9a909d54cfc264306b7d5f6d7779cffe1</sha1>
  </revision>
  <revision>
    <id>88</id>
    <parentid>87</parentid>
    <timestamp>2023-11-05T20:23:10Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1496" xml:space="preserve">In order to properly configure your database you need to edit some of the configuration files:

* open the file ''initialize/db.inc.php'' in a text editor and edit the values of the following variables:
** &lt;code&gt;$databaseName&lt;/code&gt; must contain the name of your MySQL database (example: "literature")
** &lt;code&gt;$username&lt;/code&gt; must contain the name of the MySQL user that's used with your MySQL database (example: "litwww")
** &lt;code&gt;$password&lt;/code&gt; must contain the password that's required to access your MySQL database (example: "%l1t3ratur3?")
* similarly, open the file ''initialize/ini.inc.php'' and edit all values of the contained variables to fit your needs (please see the comments within the file for further guidance)

Note that the refbase ''install.php'' script adds a new MySQL user to the MySQL database which is appropriate for use with the refbase application ([[Add MySQL User|more info]]).

== Shared database ==

If you are not able to create a new database for your refbase install, you must check that any existing database you configure does not contain tables whose names conflict with the [[MySQL tables]] used by refbase. refbase table names are specified in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') and can be changed there to avoid any name conflicts with existing tables. See [[Installing refbase#Installation over an existing database|Installation over an existing database]] for more info.

[[Category:Installation]]
__NOEDITSECTION__</text>
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<page arvcontinue="20231026120622|54">
  <title>Add MySQL User</title>
  <ns>0</ns>
  <id>27</id>
  <revision>
    <id>89</id>
    <timestamp>2023-11-05T20:28:36Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 07-Feb-2006</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1319" xml:space="preserve">To avoid any security risks the refbase ''install.php'' script adds a new MySQL user to the MySQL database during installation. This user is granted only those permissions that are required to access the literature database. If you want to add this MySQL user manually (i.e. without ''install.php''), run the MySQL command interpreter with root permissions and use the following &lt;code&gt;GRANT&lt;/code&gt; statement:

 GRANT SELECT,INSERT,UPDATE,DELETE ON ''MYSQL_DATABASE_NAME_GOES_HERE''.* TO ''MYSQL_USER_NAME_GOES_HERE''@localhost IDENTIFIED BY '''MYSQL_PASSWORD_GOES_HERE''';

The italic items within the above statement must match the information you've provided in ''initialize/db.inc.php''. As an example, if you've entered the following in ''initialize/db.inc.php'':

 $hostName = "localhost";
 $databaseName = "literature";
 $username = "litwww";
 $password = "%l1t3ratur3?";

your &lt;code&gt;GRANT&lt;/code&gt; statement would read:

 GRANT SELECT,INSERT,UPDATE,DELETE ON literature.* TO litwww@localhost IDENTIFIED BY '%l1t3ratur3?';

This adds a new user ''litwww'' to the ''user'' &amp; ''db'' tables of the ''mysql'' database and allows him to use only the SQL statements &lt;code&gt;SELECT&lt;/code&gt;, &lt;code&gt;INSERT&lt;/code&gt;, &lt;code&gt;UPDATE&lt;/code&gt; and &lt;code&gt;DELETE&lt;/code&gt; with any table of the literature database.

[[Category:Installation]]</text>
    <sha1>6ca58630039102730a4a65711ee44e4cee992980</sha1>
  </revision>
  <revision>
    <id>90</id>
    <parentid>89</parentid>
    <timestamp>2023-11-05T20:34:00Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Fix incorrect wiki formatting in GRANT statement</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1353" xml:space="preserve">To avoid any security risks the refbase ''install.php'' script adds a new MySQL user to the MySQL database during installation. This user is granted only those permissions that are required to access the literature database. If you want to add this MySQL user manually (i.e. without ''install.php''), run the MySQL command interpreter with root permissions and use the following &lt;code&gt;GRANT&lt;/code&gt; statement:

 GRANT SELECT,INSERT,UPDATE,DELETE ON ''MYSQL_DATABASE_NAME_GOES_HERE''.* TO ''MYSQL_USER_NAME_GOES_HERE''@localhost IDENTIFIED BY &lt;nowiki&gt;'&lt;/nowiki&gt;''MYSQL_PASSWORD_GOES_HERE''&lt;nowiki&gt;'&lt;/nowiki&gt;;

The italic items within the above statement must match the information you've provided in ''initialize/db.inc.php''. As an example, if you've entered the following in ''initialize/db.inc.php'':

 $hostName = "localhost";
 $databaseName = "literature";
 $username = "litwww";
 $password = "%l1t3ratur3?";

your &lt;code&gt;GRANT&lt;/code&gt; statement would read:

 GRANT SELECT,INSERT,UPDATE,DELETE ON literature.* TO litwww@localhost IDENTIFIED BY '%l1t3ratur3?';

This adds a new user ''litwww'' to the ''user'' &amp; ''db'' tables of the ''mysql'' database and allows him to use only the SQL statements &lt;code&gt;SELECT&lt;/code&gt;, &lt;code&gt;INSERT&lt;/code&gt;, &lt;code&gt;UPDATE&lt;/code&gt; and &lt;code&gt;DELETE&lt;/code&gt; with any table of the literature database.

[[Category:Installation]]</text>
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</page>
<page arvcontinue="20231026120622|54">
  <title>MySQL tables</title>
  <ns>0</ns>
  <id>28</id>
  <revision>
    <id>91</id>
    <timestamp>2023-11-05T20:36:40Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 13-Mar-2007</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2144" xml:space="preserve">MySQL tables used by refbase:

* [[Table auth|auth]]
* [[Table deleted|deleted]]
* [[Table depends|depends]]
* [[Table formats|formats]]
* [[Table languages|languages]]
* [[Table queries|queries]]
* [[Table refs|refs]]
* [[Table styles|styles]]
* [[Table types|types]]
* [[Table user_data|user_data]]
* [[Table user_formats|user_formats]]
* [[Table user_options|user_options]]
* [[Table user_permissions|user_permissions]]
* [[Table user_styles|user_styles]]
* [[Table user_types|user_types]]
* [[Table users|users]]

== Note ==

As of refbase 0.9.0 installation via the web interface (''install.php'') does not offer to set a MySQL table prefix which permits multiple instances of refbase to coexist within a single database, or to install refbase into an existing database. However, refbase table names can be renamed in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') to avoid any name conflicts with existing database tables. See [[Installing refbase#Installation over an existing database|Installation over an existing database]] for more info.

=== Listing existing MySQL tables ===

The following command illustrates one method to list the tables contained in an existing MySQL database using the &lt;code&gt;[http://dev.mysql.com/doc/refman/5.0/en/mysqlshow.html mysqlshow]&lt;/code&gt; command. 

 mysqlshow -h DATABASE.SERVER.COM -u USER_NAME -p DATABASE_NAME

Items in uppercase must be adjusted to suit your setup. The &lt;code&gt;-h DATABASE.SERVER.COM&lt;/code&gt; argument is not required to access a database on a localhost. A &lt;code&gt;USER_NAME&lt;/code&gt; with read permission suffices. Note that MySQL special characters in the &lt;code&gt;DATABASE_NAME&lt;/code&gt; (such as the _ underscore character) require shell escapes. Example: With ''litwww'' being an authorized MySQL user and ''literature'' as the name of your local refbase database, your command would read:

 mysqlshow -h localhost -u litwww -p literature

Alternatively, you could use a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or run the MySQL command line interpreter and execute this MySQL command:

 show tables from DATABASE_NAME;

[[Category:Database Information]]</text>
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    <id>92</id>
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    <model>wikitext</model>
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    <text bytes="2162" xml:space="preserve">MySQL tables used by refbase:

* [[Table auth|auth]]
* [[Table deleted|deleted]]
* [[Table depends|depends]]
* [[Table formats|formats]]
* [[Table languages|languages]]
* [[Table queries|queries]]
* [[Table refs|refs]]
* [[Table styles|styles]]
* [[Table types|types]]
* [[Table user_data|user_data]]
* [[Table user_formats|user_formats]]
* [[Table user_options|user_options]]
* [[Table user_permissions|user_permissions]]
* [[Table user_styles|user_styles]]
* [[Table user_types|user_types]]
* [[Table users|users]]

== Note ==

As of refbase 0.9.0 installation via the web interface (''install.php'') does not offer to set a MySQL table prefix which permits multiple instances of refbase to coexist within a single database, or to install refbase into an existing database. However, refbase table names can be renamed in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') to avoid any name conflicts with existing database tables. See [[Installing refbase#Installation over an existing database|Installation over an existing database]] for more info.

=== Listing existing MySQL tables ===

The following command illustrates one method to list the tables contained in an existing MySQL database using the &lt;code&gt;[http://dev.mysql.com/doc/refman/5.0/en/mysqlshow.html mysqlshow]&lt;/code&gt; command. 

 mysqlshow -h DATABASE.SERVER.COM -u USER_NAME -p DATABASE_NAME

Items in uppercase must be adjusted to suit your setup. The &lt;code&gt;-h DATABASE.SERVER.COM&lt;/code&gt; argument is not required to access a database on a localhost. A &lt;code&gt;USER_NAME&lt;/code&gt; with read permission suffices. Note that MySQL special characters in the &lt;code&gt;DATABASE_NAME&lt;/code&gt; (such as the _ underscore character) require shell escapes. Example: With ''litwww'' being an authorized MySQL user and ''literature'' as the name of your local refbase database, your command would read:

 mysqlshow -h localhost -u litwww -p literature

Alternatively, you could use a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or run the MySQL command line interpreter and execute this MySQL command:

 show tables from DATABASE_NAME;

[[Category:Database Information]]
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    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2163" xml:space="preserve">MySQL tables used by refbase:

* [[Table auth|auth]]
* [[Table deleted|deleted]]
* [[Table depends|depends]]
* [[Table formats|formats]]
* [[Table languages|languages]]
* [[Table queries|queries]]
* [[Table refs|refs]]
* [[Table styles|styles]]
* [[Table types|types]]
* [[Table user_data|user_data]]
* [[Table user_formats|user_formats]]
* [[Table user_options|user_options]]
* [[Table user_permissions|user_permissions]]
* [[Table user_styles|user_styles]]
* [[Table user_types|user_types]]
* [[Table users|users]]

== Note ==

As of refbase 0.9.0 installation via the web interface (''install.php'') does not offer to set a MySQL table prefix which permits multiple instances of refbase to coexist within a single database, or to install refbase into an existing database. However, refbase table names can be renamed in files ''initialize/db.inc.php'' &amp; ''install.sql'' (or ''update.sql'') to avoid any name conflicts with existing database tables. See [[Installing refbase#Installation over an existing database|Installation over an existing database]] for more info.

=== Listing existing MySQL tables ===

The following command illustrates one method to list the tables contained in an existing MySQL database using the &lt;code&gt;[https://dev.mysql.com/doc/refman/8.0/en/mysqlshow.html mysqlshow]&lt;/code&gt; command. 

 mysqlshow -h DATABASE.SERVER.COM -u USER_NAME -p DATABASE_NAME

Items in uppercase must be adjusted to suit your setup. The &lt;code&gt;-h DATABASE.SERVER.COM&lt;/code&gt; argument is not required to access a database on a localhost. A &lt;code&gt;USER_NAME&lt;/code&gt; with read permission suffices. Note that MySQL special characters in the &lt;code&gt;DATABASE_NAME&lt;/code&gt; (such as the _ underscore character) require shell escapes. Example: With ''litwww'' being an authorized MySQL user and ''literature'' as the name of your local refbase database, your command would read:

 mysqlshow -h localhost -u litwww -p literature

Alternatively, you could use a tool such as [http://www.phpmyadmin.net/ phpMyAdmin] or run the MySQL command line interpreter and execute this MySQL command:

 show tables from DATABASE_NAME;

[[Category:Database Information]]
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    <text bytes="16616" xml:space="preserve">&lt;p&gt;This table lists all field names &amp;amp; column types for the MySQL database table 'refs' that's used in conjunction with refbase 0.8.0:&lt;/p&gt;

&lt;table border="0" cellspacing="10"&gt;
&lt;tr valign="top"&gt;&lt;th align="left"&gt;Field&lt;/th&gt;&lt;th align="left"&gt;Type&lt;/th&gt;&lt;th align="left"&gt;Example&lt;/th&gt;&lt;th align="left"&gt;Comment&lt;/th&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;author&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Clough, LM; de Broyer, H-C; Ambrose Jr., WG&lt;/td&gt;&lt;td&gt;The author(s) of a publication. Separate family and given names with a comma &amp;amp; a space (', '). Multiple authors are separated with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;address&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK, mailto:author@geos.com&lt;/td&gt;&lt;td&gt;The author's address or any other contact information like the email of the corresponding author. Separate multiple addresses with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;corporate_author&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;University of California&lt;/td&gt;&lt;td&gt;Use this field when the author of a particular publication is not a person, but an organization, government agency, company or other group. The personal author (if there is one) is subordinate to the organisation. In the case of a thesis, the student's institution (or university) can be regarded as the corporate author of the student's work. Sometimes, the corporate author is identical to the publisher of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;first_author&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Clough, LM&lt;/td&gt;&lt;td&gt;This field holds the family and given name of the first author. It is required for proper sorting of references when citing. On edit refbase will automatically extract the first author from the &lt;code&gt;author&lt;/code&gt; field and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;author_count&lt;/code&gt;&lt;/td&gt;&lt;td&gt;tinyint(3) unsigned&lt;/td&gt;&lt;td&gt;3&lt;/td&gt;&lt;td&gt;The number of authors of a publication. It is required for proper sorting of references when citing. On edit refbase will automatically assign the correct author count to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Life and benthic environment in the Barents Sea&lt;/td&gt;&lt;td&gt;The title of a publication; don't append any dot to the title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;orig_title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Zhizn' i usloviya ee sushchestvovaniya v bentali Barentseva morya&lt;/td&gt;&lt;td&gt;Use this field for the original title of a publication if the title given in the &lt;code&gt;title&lt;/code&gt; field is a translated or transliterated version of the original title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;publication&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Marine Ecology Progress Series&lt;/td&gt;&lt;td&gt;The full title of the journal or the book title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;abbrev_journal&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Mar Ecol Prog Ser&lt;/td&gt;&lt;td&gt;In case of journals, the abbreviated journal title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;year&lt;/code&gt;&lt;/td&gt;&lt;td&gt;smallint(6)&lt;/td&gt;&lt;td&gt;1998&lt;/td&gt;&lt;td&gt;The publication year; specify years in 4-digit format.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;volume&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;56A&lt;/td&gt;&lt;td&gt;The volume of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;volume_numeric&lt;/code&gt;&lt;/td&gt;&lt;td&gt;smallint(5) unsigned&lt;/td&gt;&lt;td&gt;56&lt;/td&gt;&lt;td&gt;The number part of the publication volume. refbase uses this field when sorting by &lt;code&gt;volume&lt;/code&gt;. While the &lt;code&gt;volume&lt;/code&gt; field accepts any text the field &lt;code&gt;volume_numeric&lt;/code&gt; is of numeric type and can only contain numbers. On edit refbase will automatically extract the first number from field &lt;code&gt;volume&lt;/code&gt; and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;issue&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;4&lt;/td&gt;&lt;td&gt;The issue (i.e. number) of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;pages&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;12-18&lt;/td&gt;&lt;td&gt;The page range (or total number of pages) of a publication. For journal articles &amp;amp; book chapters use the page range like in '12-18' (no 'pp'), for whole books enter the total no. of pages like in '316 pp' (i.e. append 'pp')&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;first_page&lt;/code&gt;&lt;/td&gt;&lt;td&gt;mediumint(8) unsigned&lt;/td&gt;&lt;td&gt;12&lt;/td&gt;&lt;td&gt;The first page of a publication (for journal articles or book chapters) or the total no. of pages in case of whole books. refbase uses this field when sorting by &lt;code&gt;pages&lt;/code&gt;. On edit refbase will automatically extract the first number from field &lt;code&gt;pages&lt;/code&gt; and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;keywords&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;sea ice; flooding; primary productivity; PS, Antarctic Ocean; PSW, Weddell Sea&lt;/td&gt;&lt;td&gt;Any keywords given by the authors of the publication. A user's personal keywords should be entered in the user-specific field &lt;code&gt;user_keys&lt;/code&gt; (MySQL table 'user_data'). Separate multiple (unrelated) keywords with a semicolon &amp;amp; a space ('; '), if some keywords are somehow related, you may optionally separate them with a comma &amp;amp; a space (', ') instead.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;abstract&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Organic matter displayed a pronounced seasonal variation in carbon isotopes (expressed as [delta][super:13]C_[sub:OM]_).&lt;/td&gt;&lt;td&gt;The abstract or summary of the publication. The &lt;code&gt;title&lt;/code&gt;, &lt;code&gt;address&lt;/code&gt;, &lt;code&gt;keywords&lt;/code&gt; and &lt;code&gt;abstract&lt;/code&gt; fields support a markup language to provide rich text capabilities (i.e. italics, super/sub-script, greek letters, etc). E.g., the markup in the example would display as &amp;delta;&lt;sup&gt;13&lt;/sup&gt;C&lt;i&gt;&lt;sub&gt;OM&lt;/sub&gt;&lt;/i&gt;. See [[Refbase markup syntax]] as well as the file &lt;em&gt;initialize/ini.inc.php&lt;/em&gt; for further information.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;edition&lt;/code&gt;&lt;/td&gt;&lt;td&gt;tinyint(3) unsigned&lt;/td&gt;&lt;td&gt;2&lt;/td&gt;&lt;td&gt;The edition number of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;editor&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Ackley, SF; Weeks, WF&lt;/td&gt;&lt;td&gt;The editor(s) of a publication. Format names as described for field &lt;code&gt;author&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;publisher&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;American Geophysical Union&lt;/td&gt;&lt;td&gt;The publisher of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;place&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Washington, DC&lt;/td&gt;&lt;td&gt;The place of publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;medium&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;CD-ROM&lt;/td&gt;&lt;td&gt;Contains the medium type of a publication if not paper (e.g. CD-ROM, cassettes, disks, transparencies, negatives, slides, etc.)&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_editor&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Strelkov, A&lt;/td&gt;&lt;td&gt;The series editor(s). Format names as described for field &lt;code&gt;author&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;UNESCO Monographs on Oceanographic Methodology&lt;/td&gt;&lt;td&gt;If the publication is part of a series, this field holds the full title of the series.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;abbrev_series_title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;UNESCO Monogr Oceanogr Methodol&lt;/td&gt;&lt;td&gt;The abbreviated series title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_volume&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;6&lt;/td&gt;&lt;td&gt;The series volume of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_volume_numeric&lt;/code&gt;&lt;/td&gt;&lt;td&gt;smallint(5) unsigned&lt;/td&gt;&lt;td&gt;6&lt;/td&gt;&lt;td&gt;The number part of the series volume. refbase uses this field when sorting by &lt;code&gt;series_volume&lt;/code&gt;. While the &lt;code&gt;series_volume&lt;/code&gt; field accepts any text the field &lt;code&gt;series_volume_numeric&lt;/code&gt; is of numeric type and can only contain numbers. On edit refbase will automatically extract the first number from field &lt;code&gt;series_volume&lt;/code&gt; and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_issue&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;II&lt;/td&gt;&lt;td&gt;The issue (i.e. number) of the series volume.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;issn&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;0148-0227&lt;/td&gt;&lt;td&gt;If the publication is (part of) a journal or a dissertation, specify it's ISSN number in this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;isbn&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;0-12-026143-X&lt;/td&gt;&lt;td&gt;If the publication is a book (chapter), specify it's ISBN number in this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;language&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Russian&lt;/td&gt;&lt;td&gt;The language of the body text.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;summary_language&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;English; Russian&lt;/td&gt;&lt;td&gt;The language of the summary or abstract. Separate multiple language identifiers with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;area&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Antarctic; McMurdo Sound&lt;/td&gt;&lt;td&gt;The area of investigation this publication deals with. Multiple items should be separated with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;type&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Journal Article&lt;/td&gt;&lt;td&gt;The reference type of a publication. By default refbase recognizes 'Journal Article', 'Book Chapter', 'Book Whole', 'Journal', 'Manuscript' and 'Map'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;thesis&lt;/code&gt;&lt;/td&gt;&lt;td&gt;enum("Bachelor's thesis","Master's thesis","Ph.D. thesis","Diploma thesis","Doctoral thesis","Habilitation thesis")&lt;/td&gt;&lt;td&gt;Ph.D. thesis&lt;/td&gt;&lt;td&gt;If the publication is a thesis, specify the degree in this field. By default refbase recognizes 'Bachelor&amp;rsquo;s thesis', 'Master&amp;rsquo;s thesis', 'Ph.D. thesis', 'Diploma thesis', 'Doctoral thesis' and 'Habilitation thesis'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;expedition&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Norwegian Antarctic Research Expedition (NARE) 2000/2001&lt;/td&gt;&lt;td&gt;The name of the expedition where sampling took place.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;doi&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;10.1007/s00300-004-0674-5&lt;/td&gt;&lt;td&gt;The unique [http://www.doi.org/ Digital Object Identifier] (DOI) of this publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;conference&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;International Symposium on Polar Aspects of Global Change, Troms&amp;oslash; (Norway), 24-28 Aug 1998&lt;/td&gt;&lt;td&gt;The conference this publication was initially presented at.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;url&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;http://www.int-res.com/abstracts/meps/v251/p37-47.html&lt;/td&gt;&lt;td&gt;The web address providing more information for this publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;call_number&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;IP&amp;Ouml; @ msteffens @ 83; IP&amp;Ouml; @ mschmid @ Be 100; AWI @ tmock @ Ice-23&lt;/td&gt;&lt;td&gt;Contains a user's identifier tag &amp;amp; personal reference number that uniquely identifies this record for the user. Multiple items should be separated with a semicolon &amp;amp; a space ('; '). This field is controlled (and automatically filled) by refbase on edit. Syntax: &lt;em&gt;institutional abbreviation&lt;/em&gt; @ &lt;em&gt;email user name&lt;/em&gt; @ &lt;em&gt;personal reference number&lt;/em&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;location&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Matthias Steffens (msteffens@ipoe.de); Michael Schmid (mschmid@ipoe.de); Thomas Mock (tmock@awi.ac.uk)&lt;/td&gt;&lt;td&gt;Contains all users who have added this record to their personal literature data set. Multiple users should be separated with a semicolon &amp;amp; a space ('; '). Like the &lt;code&gt;call_number&lt;/code&gt; field, this field is controlled (and automatically filled) by refbase on edit. Syntax: &lt;em&gt;user name&lt;/em&gt; (&lt;em&gt;email address&lt;/em&gt;)&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;contribution_id&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;IP&amp;Ouml;; AWI&lt;/td&gt;&lt;td&gt;Holds the institutional abbreviation of a database user if this publication was published by this user or a member of his institution. Multiple items must be separated with a semicolon &amp;amp; a space ('; '). Information in this field can be used to generate a dynamic web page of all publications that were published by a particular institution. See [[Auto-updating author/group bibliographies|here]] for more information.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;online_publication&lt;/code&gt;&lt;/td&gt;&lt;td&gt;enum("no","yes")&lt;/td&gt;&lt;td&gt;no&lt;/td&gt;&lt;td&gt;Set to 'yes' if this publication is an online publication that has no print equivalent (yet). Must be either 'yes' or 'no'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;online_citation&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;L09402&lt;/td&gt;&lt;td&gt;Contains any additional information that's required to locate the online location of the publication. If &lt;code&gt;online_publication&lt;/code&gt; is 'yes', the contents of this field will be printed (together with the &lt;code&gt;doi&lt;/code&gt; number) in place of &lt;code&gt;pages&lt;/code&gt; when citing.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;file&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Science295p641.pdf&lt;/td&gt;&lt;td&gt;The name of (or path to) a file that's associated with this publication (e.g. a PDF file). The &lt;code&gt;file&lt;/code&gt; field accepts full URLs (which must start with either 'http://' or 'ftp://') as well as relative or absolute paths to the file (if it's located on your server). Any string that's not a full URL will be prefixed with the string given in &lt;var&gt;$filesBaseURL&lt;/var&gt; (file &lt;em&gt;initialize/ini.inc.php&lt;/em&gt;).&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;notes&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Species identification book; richly illustrated keys with 135 tables with b/w morphological drawings&lt;/td&gt;&lt;td&gt;Any generic notes for this publication. Multiple items should be separated with a semicolon &amp;amp; a space ('; '). A user's personal notes should be entered in the user-specific field &lt;code&gt;user_notes&lt;/code&gt; (MySQL table 'user_data').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;serial&lt;/code&gt;&lt;/td&gt;&lt;td&gt;mediumint(8) unsigned&lt;/td&gt;&lt;td&gt;1297&lt;/td&gt;&lt;td&gt;The unique database serial number of the publication (i.e. the MySQL primary key). The serial number is automatically filled in by MySQL when importing/adding records and is used to uniquely identify a particular database entry.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;orig_record&lt;/code&gt;&lt;/td&gt;&lt;td&gt;mediumint(9)&lt;/td&gt;&lt;td&gt;-1297&lt;/td&gt;&lt;td&gt;In the case of duplicates, this field indicates whether this record is considered as the original record or as a duplicate entry. If it's an original record, the &lt;code&gt;orig_record&lt;/code&gt; field contains the record's own &lt;code&gt;serial&lt;/code&gt; number prefixed with a minus ('-') sign. If this record is a duplicate entry, &lt;code&gt;orig_record&lt;/code&gt; will contain the &lt;code&gt;serial&lt;/code&gt; number of the original record. By this, the &lt;code&gt;orig_record&lt;/code&gt; field can be used to flag or hide any duplicates and point to the original record instead. Currently, refbase will only flag original/duplicate records using appropriate icons.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;approved&lt;/code&gt;&lt;/td&gt;&lt;td&gt;enum("no","yes")&lt;/td&gt;&lt;td&gt;yes&lt;/td&gt;&lt;td&gt;Set to 'yes' if you've verified this record for correctness, otherwise set to 'no'. Must be either 'yes' or 'no'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;created_date&lt;/code&gt;&lt;/td&gt;&lt;td&gt;date&lt;/td&gt;&lt;td&gt;2004-12-31&lt;/td&gt;&lt;td&gt;The creation date of this record. This field is controlled (and automatically filled) by refbase when adding a record. Date format must be &lt;code&gt;YYYY-MM-DD&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;created_time&lt;/code&gt;&lt;/td&gt;&lt;td&gt;time&lt;/td&gt;&lt;td&gt;19:08:44&lt;/td&gt;&lt;td&gt;The creation time of this record. This field is controlled (and automatically filled) by refbase when adding a record. Time format must be &lt;code&gt;HH:MM:SS&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;created_by&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Matthias Steffens (msteffens@ipoe.de)&lt;/td&gt;&lt;td&gt;Contains the name and email address of the person who created this record. This field is controlled (and automatically filled) by refbase when adding a record. Syntax: &lt;em&gt;user name&lt;/em&gt; (&lt;em&gt;email address&lt;/em&gt;).&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;modified_date&lt;/code&gt;&lt;/td&gt;&lt;td&gt;date&lt;/td&gt;&lt;td&gt;2005-03-22&lt;/td&gt;&lt;td&gt;The modification date of this record. This field is controlled (and automatically filled) by refbase when editing a record. Date format must be &lt;code&gt;YYYY-MM-DD&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;modified_time&lt;/code&gt;&lt;/td&gt;&lt;td&gt;time&lt;/td&gt;&lt;td&gt;23:50:52&lt;/td&gt;&lt;td&gt;The modification time of this record. This field is controlled (and automatically filled) by refbase when editing a record. Time format must be &lt;code&gt;HH:MM:SS&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;modified_by&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Michael Schmid (mschmid@ipoe.de)&lt;/td&gt;&lt;td&gt;Contains the name and email address of the last person who modified this record. This field is controlled (and automatically filled) by refbase when editing a record. Syntax: &lt;em&gt;user name&lt;/em&gt; (&lt;em&gt;email address&lt;/em&gt;).&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;

[[Category:MySQL tables]]</text>
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    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update external links</comment>
    <model>wikitext</model>
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    <text bytes="16643" xml:space="preserve">&lt;p&gt;This table lists all field names &amp;amp; column types for the MySQL database table 'refs' that's used in conjunction with refbase 0.8.0:&lt;/p&gt;

&lt;table border="0" cellspacing="10"&gt;
&lt;tr valign="top"&gt;&lt;th align="left"&gt;Field&lt;/th&gt;&lt;th align="left"&gt;Type&lt;/th&gt;&lt;th align="left"&gt;Example&lt;/th&gt;&lt;th align="left"&gt;Comment&lt;/th&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;author&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Clough, LM; de Broyer, H-C; Ambrose Jr., WG&lt;/td&gt;&lt;td&gt;The author(s) of a publication. Separate family and given names with a comma &amp;amp; a space (', '). Multiple authors are separated with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;address&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;School of Environmental Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK, mailto:author@geos.com&lt;/td&gt;&lt;td&gt;The author's address or any other contact information like the email of the corresponding author. Separate multiple addresses with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;corporate_author&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;University of California&lt;/td&gt;&lt;td&gt;Use this field when the author of a particular publication is not a person, but an organization, government agency, company or other group. The personal author (if there is one) is subordinate to the organisation. In the case of a thesis, the student's institution (or university) can be regarded as the corporate author of the student's work. Sometimes, the corporate author is identical to the publisher of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;first_author&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Clough, LM&lt;/td&gt;&lt;td&gt;This field holds the family and given name of the first author. It is required for proper sorting of references when citing. On edit refbase will automatically extract the first author from the &lt;code&gt;author&lt;/code&gt; field and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;author_count&lt;/code&gt;&lt;/td&gt;&lt;td&gt;tinyint(3) unsigned&lt;/td&gt;&lt;td&gt;3&lt;/td&gt;&lt;td&gt;The number of authors of a publication. It is required for proper sorting of references when citing. On edit refbase will automatically assign the correct author count to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Life and benthic environment in the Barents Sea&lt;/td&gt;&lt;td&gt;The title of a publication; don't append any dot to the title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;orig_title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Zhizn' i usloviya ee sushchestvovaniya v bentali Barentseva morya&lt;/td&gt;&lt;td&gt;Use this field for the original title of a publication if the title given in the &lt;code&gt;title&lt;/code&gt; field is a translated or transliterated version of the original title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;publication&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Marine Ecology Progress Series&lt;/td&gt;&lt;td&gt;The full title of the journal or the book title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;abbrev_journal&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Mar Ecol Prog Ser&lt;/td&gt;&lt;td&gt;In case of journals, the abbreviated journal title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;year&lt;/code&gt;&lt;/td&gt;&lt;td&gt;smallint(6)&lt;/td&gt;&lt;td&gt;1998&lt;/td&gt;&lt;td&gt;The publication year; specify years in 4-digit format.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;volume&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;56A&lt;/td&gt;&lt;td&gt;The volume of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;volume_numeric&lt;/code&gt;&lt;/td&gt;&lt;td&gt;smallint(5) unsigned&lt;/td&gt;&lt;td&gt;56&lt;/td&gt;&lt;td&gt;The number part of the publication volume. refbase uses this field when sorting by &lt;code&gt;volume&lt;/code&gt;. While the &lt;code&gt;volume&lt;/code&gt; field accepts any text the field &lt;code&gt;volume_numeric&lt;/code&gt; is of numeric type and can only contain numbers. On edit refbase will automatically extract the first number from field &lt;code&gt;volume&lt;/code&gt; and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;issue&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;4&lt;/td&gt;&lt;td&gt;The issue (i.e. number) of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;pages&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;12-18&lt;/td&gt;&lt;td&gt;The page range (or total number of pages) of a publication. For journal articles &amp;amp; book chapters use the page range like in '12-18' (no 'pp'), for whole books enter the total no. of pages like in '316 pp' (i.e. append 'pp')&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;first_page&lt;/code&gt;&lt;/td&gt;&lt;td&gt;mediumint(8) unsigned&lt;/td&gt;&lt;td&gt;12&lt;/td&gt;&lt;td&gt;The first page of a publication (for journal articles or book chapters) or the total no. of pages in case of whole books. refbase uses this field when sorting by &lt;code&gt;pages&lt;/code&gt;. On edit refbase will automatically extract the first number from field &lt;code&gt;pages&lt;/code&gt; and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;keywords&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;sea ice; flooding; primary productivity; PS, Antarctic Ocean; PSW, Weddell Sea&lt;/td&gt;&lt;td&gt;Any keywords given by the authors of the publication. A user's personal keywords should be entered in the user-specific field &lt;code&gt;user_keys&lt;/code&gt; (MySQL table 'user_data'). Separate multiple (unrelated) keywords with a semicolon &amp;amp; a space ('; '), if some keywords are somehow related, you may optionally separate them with a comma &amp;amp; a space (', ') instead.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;abstract&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Organic matter displayed a pronounced seasonal variation in carbon isotopes (expressed as [delta][super:13]C_[sub:OM]_).&lt;/td&gt;&lt;td&gt;The abstract or summary of the publication. The &lt;code&gt;title&lt;/code&gt;, &lt;code&gt;address&lt;/code&gt;, &lt;code&gt;keywords&lt;/code&gt; and &lt;code&gt;abstract&lt;/code&gt; fields support a markup language to provide rich text capabilities (i.e. italics, super/sub-script, greek letters, etc). E.g., the markup in the example would display as &amp;delta;&lt;sup&gt;13&lt;/sup&gt;C&lt;i&gt;&lt;sub&gt;OM&lt;/sub&gt;&lt;/i&gt;. See [[Refbase markup syntax]] as well as the file &lt;em&gt;initialize/ini.inc.php&lt;/em&gt; for further information.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;edition&lt;/code&gt;&lt;/td&gt;&lt;td&gt;tinyint(3) unsigned&lt;/td&gt;&lt;td&gt;2&lt;/td&gt;&lt;td&gt;The edition number of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;editor&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Ackley, SF; Weeks, WF&lt;/td&gt;&lt;td&gt;The editor(s) of a publication. Format names as described for field &lt;code&gt;author&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;publisher&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;American Geophysical Union&lt;/td&gt;&lt;td&gt;The publisher of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;place&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Washington, DC&lt;/td&gt;&lt;td&gt;The place of publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;medium&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;CD-ROM&lt;/td&gt;&lt;td&gt;Contains the medium type of a publication if not paper (e.g. CD-ROM, cassettes, disks, transparencies, negatives, slides, etc.)&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_editor&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Strelkov, A&lt;/td&gt;&lt;td&gt;The series editor(s). Format names as described for field &lt;code&gt;author&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;UNESCO Monographs on Oceanographic Methodology&lt;/td&gt;&lt;td&gt;If the publication is part of a series, this field holds the full title of the series.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;abbrev_series_title&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;UNESCO Monogr Oceanogr Methodol&lt;/td&gt;&lt;td&gt;The abbreviated series title.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_volume&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;6&lt;/td&gt;&lt;td&gt;The series volume of a publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_volume_numeric&lt;/code&gt;&lt;/td&gt;&lt;td&gt;smallint(5) unsigned&lt;/td&gt;&lt;td&gt;6&lt;/td&gt;&lt;td&gt;The number part of the series volume. refbase uses this field when sorting by &lt;code&gt;series_volume&lt;/code&gt;. While the &lt;code&gt;series_volume&lt;/code&gt; field accepts any text the field &lt;code&gt;series_volume_numeric&lt;/code&gt; is of numeric type and can only contain numbers. On edit refbase will automatically extract the first number from field &lt;code&gt;series_volume&lt;/code&gt; and copy it to this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;series_issue&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(50)&lt;/td&gt;&lt;td&gt;II&lt;/td&gt;&lt;td&gt;The issue (i.e. number) of the series volume.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;issn&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;0148-0227&lt;/td&gt;&lt;td&gt;If the publication is (part of) a journal or a dissertation, specify it's ISSN number in this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;isbn&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;0-12-026143-X&lt;/td&gt;&lt;td&gt;If the publication is a book (chapter), specify it's ISBN number in this field.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;language&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Russian&lt;/td&gt;&lt;td&gt;The language of the body text.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;summary_language&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;English; Russian&lt;/td&gt;&lt;td&gt;The language of the summary or abstract. Separate multiple language identifiers with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;area&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Antarctic; McMurdo Sound&lt;/td&gt;&lt;td&gt;The area of investigation this publication deals with. Multiple items should be separated with a semicolon &amp;amp; a space ('; ').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;type&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Journal Article&lt;/td&gt;&lt;td&gt;The reference type of a publication. By default refbase recognizes 'Journal Article', 'Book Chapter', 'Book Whole', 'Journal', 'Manuscript' and 'Map'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;thesis&lt;/code&gt;&lt;/td&gt;&lt;td&gt;enum("Bachelor's thesis","Master's thesis","Ph.D. thesis","Diploma thesis","Doctoral thesis","Habilitation thesis")&lt;/td&gt;&lt;td&gt;Ph.D. thesis&lt;/td&gt;&lt;td&gt;If the publication is a thesis, specify the degree in this field. By default refbase recognizes 'Bachelor&amp;rsquo;s thesis', 'Master&amp;rsquo;s thesis', 'Ph.D. thesis', 'Diploma thesis', 'Doctoral thesis' and 'Habilitation thesis'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;expedition&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Norwegian Antarctic Research Expedition (NARE) 2000/2001&lt;/td&gt;&lt;td&gt;The name of the expedition where sampling took place.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;doi&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;10.1007/s00300-004-0674-5&lt;/td&gt;&lt;td&gt;The unique [https://www.doi.org/the-identifier/what-is-a-doi/ Digital Object Identifier] (DOI) of this publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;conference&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;International Symposium on Polar Aspects of Global Change, Troms&amp;oslash; (Norway), 24-28 Aug 1998&lt;/td&gt;&lt;td&gt;The conference this publication was initially presented at.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;url&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;https://www.int-res.com/abstracts/meps/v251/p37-47/&lt;/td&gt;&lt;td&gt;The web address providing more information for this publication.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;call_number&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;IP&amp;Ouml; @ msteffens @ 83; IP&amp;Ouml; @ mschmid @ Be 100; AWI @ tmock @ Ice-23&lt;/td&gt;&lt;td&gt;Contains a user's identifier tag &amp;amp; personal reference number that uniquely identifies this record for the user. Multiple items should be separated with a semicolon &amp;amp; a space ('; '). This field is controlled (and automatically filled) by refbase on edit. Syntax: &lt;em&gt;institutional abbreviation&lt;/em&gt; @ &lt;em&gt;email user name&lt;/em&gt; @ &lt;em&gt;personal reference number&lt;/em&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;location&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Matthias Steffens (msteffens@ipoe.de); Michael Schmid (mschmid@ipoe.de); Thomas Mock (tmock@awi.ac.uk)&lt;/td&gt;&lt;td&gt;Contains all users who have added this record to their personal literature data set. Multiple users should be separated with a semicolon &amp;amp; a space ('; '). Like the &lt;code&gt;call_number&lt;/code&gt; field, this field is controlled (and automatically filled) by refbase on edit. Syntax: &lt;em&gt;user name&lt;/em&gt; (&lt;em&gt;email address&lt;/em&gt;)&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;contribution_id&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;IP&amp;Ouml;; AWI&lt;/td&gt;&lt;td&gt;Holds the institutional abbreviation of a database user if this publication was published by this user or a member of his institution. Multiple items must be separated with a semicolon &amp;amp; a space ('; '). Information in this field can be used to generate a dynamic web page of all publications that were published by a particular institution. See [[Auto-updating author/group bibliographies|here]] for more information.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;online_publication&lt;/code&gt;&lt;/td&gt;&lt;td&gt;enum("no","yes")&lt;/td&gt;&lt;td&gt;no&lt;/td&gt;&lt;td&gt;Set to 'yes' if this publication is an online publication that has no print equivalent (yet). Must be either 'yes' or 'no'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;online_citation&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;L09402&lt;/td&gt;&lt;td&gt;Contains any additional information that's required to locate the online location of the publication. If &lt;code&gt;online_publication&lt;/code&gt; is 'yes', the contents of this field will be printed (together with the &lt;code&gt;doi&lt;/code&gt; number) in place of &lt;code&gt;pages&lt;/code&gt; when citing.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;file&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(255)&lt;/td&gt;&lt;td&gt;Science295p641.pdf&lt;/td&gt;&lt;td&gt;The name of (or path to) a file that's associated with this publication (e.g. a PDF file). The &lt;code&gt;file&lt;/code&gt; field accepts full URLs (which must start with either 'http://' or 'ftp://') as well as relative or absolute paths to the file (if it's located on your server). Any string that's not a full URL will be prefixed with the string given in &lt;var&gt;$filesBaseURL&lt;/var&gt; (file &lt;em&gt;initialize/ini.inc.php&lt;/em&gt;).&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;notes&lt;/code&gt;&lt;/td&gt;&lt;td&gt;text&lt;/td&gt;&lt;td&gt;Species identification book; richly illustrated keys with 135 tables with b/w morphological drawings&lt;/td&gt;&lt;td&gt;Any generic notes for this publication. Multiple items should be separated with a semicolon &amp;amp; a space ('; '). A user's personal notes should be entered in the user-specific field &lt;code&gt;user_notes&lt;/code&gt; (MySQL table 'user_data').&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;serial&lt;/code&gt;&lt;/td&gt;&lt;td&gt;mediumint(8) unsigned&lt;/td&gt;&lt;td&gt;1297&lt;/td&gt;&lt;td&gt;The unique database serial number of the publication (i.e. the MySQL primary key). The serial number is automatically filled in by MySQL when importing/adding records and is used to uniquely identify a particular database entry.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;orig_record&lt;/code&gt;&lt;/td&gt;&lt;td&gt;mediumint(9)&lt;/td&gt;&lt;td&gt;-1297&lt;/td&gt;&lt;td&gt;In the case of duplicates, this field indicates whether this record is considered as the original record or as a duplicate entry. If it's an original record, the &lt;code&gt;orig_record&lt;/code&gt; field contains the record's own &lt;code&gt;serial&lt;/code&gt; number prefixed with a minus ('-') sign. If this record is a duplicate entry, &lt;code&gt;orig_record&lt;/code&gt; will contain the &lt;code&gt;serial&lt;/code&gt; number of the original record. By this, the &lt;code&gt;orig_record&lt;/code&gt; field can be used to flag or hide any duplicates and point to the original record instead. Currently, refbase will only flag original/duplicate records using appropriate icons.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;approved&lt;/code&gt;&lt;/td&gt;&lt;td&gt;enum("no","yes")&lt;/td&gt;&lt;td&gt;yes&lt;/td&gt;&lt;td&gt;Set to 'yes' if you've verified this record for correctness, otherwise set to 'no'. Must be either 'yes' or 'no'.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;created_date&lt;/code&gt;&lt;/td&gt;&lt;td&gt;date&lt;/td&gt;&lt;td&gt;2004-12-31&lt;/td&gt;&lt;td&gt;The creation date of this record. This field is controlled (and automatically filled) by refbase when adding a record. Date format must be &lt;code&gt;YYYY-MM-DD&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;created_time&lt;/code&gt;&lt;/td&gt;&lt;td&gt;time&lt;/td&gt;&lt;td&gt;19:08:44&lt;/td&gt;&lt;td&gt;The creation time of this record. This field is controlled (and automatically filled) by refbase when adding a record. Time format must be &lt;code&gt;HH:MM:SS&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;created_by&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Matthias Steffens (msteffens@ipoe.de)&lt;/td&gt;&lt;td&gt;Contains the name and email address of the person who created this record. This field is controlled (and automatically filled) by refbase when adding a record. Syntax: &lt;em&gt;user name&lt;/em&gt; (&lt;em&gt;email address&lt;/em&gt;).&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;modified_date&lt;/code&gt;&lt;/td&gt;&lt;td&gt;date&lt;/td&gt;&lt;td&gt;2005-03-22&lt;/td&gt;&lt;td&gt;The modification date of this record. This field is controlled (and automatically filled) by refbase when editing a record. Date format must be &lt;code&gt;YYYY-MM-DD&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;modified_time&lt;/code&gt;&lt;/td&gt;&lt;td&gt;time&lt;/td&gt;&lt;td&gt;23:50:52&lt;/td&gt;&lt;td&gt;The modification time of this record. This field is controlled (and automatically filled) by refbase when editing a record. Time format must be &lt;code&gt;HH:MM:SS&lt;/code&gt;.&lt;/td&gt;&lt;/tr&gt;
&lt;tr valign="top"&gt;&lt;td&gt;&lt;code&gt;modified_by&lt;/code&gt;&lt;/td&gt;&lt;td&gt;varchar(100)&lt;/td&gt;&lt;td&gt;Michael Schmid (mschmid@ipoe.de)&lt;/td&gt;&lt;td&gt;Contains the name and email address of the last person who modified this record. This field is controlled (and automatically filled) by refbase when editing a record. Syntax: &lt;em&gt;user name&lt;/em&gt; (&lt;em&gt;email address&lt;/em&gt;).&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;

[[Category:MySQL tables]]</text>
    <sha1>e37368baa2dc640211d061adb09882012a80ffd5</sha1>
  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Installation-Troubleshooting</title>
  <ns>0</ns>
  <id>30</id>
  <revision>
    <id>96</id>
    <timestamp>2023-11-05T22:04:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 31-Oct-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14467" xml:space="preserve">This document presents solutions &amp; tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_Portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_Portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that &lt;code&gt;safe_mode&lt;/code&gt; is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
 error_reporting  =  E_ALL
 display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue. 
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the &lt;code&gt;phpinfo()&lt;/code&gt; function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; in your active ''php.ini'' file. The values given for &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [http://xampp.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

 upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

 upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [http://xampp.org/ XAMPP] the needed PHP function &lt;code&gt;iconv&lt;/code&gt; is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for &lt;code&gt;iconv&lt;/code&gt; and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.  

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table.  The &lt;code&gt;depends_path&lt;/code&gt; for the &lt;code&gt;bibutils&lt;/code&gt; record should '''not''' be &lt;code&gt;NULL&lt;/code&gt; as seen below:  

&lt;pre&gt;
mysql&gt; SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
|          1 | refbase          | true            | NULL         |
|          2 | bibutils         | true            | NULL         |
+------------+------------------+-----------------+--------------+
&lt;/pre&gt;

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;
* the PHP temp/session directory must be accessible &amp; writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable &lt;code&gt;$sessionTempDir&lt;/code&gt; in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3631
 
 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

 There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_Portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_Portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experience on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:  

&lt;pre&gt;
if (!function_exists('iconv') &amp;&amp; function_exists('libiconv')) {
   function iconv($input_encoding, $output_encoding, $string) {
       return libiconv($input_encoding, $output_encoding, $string);
   }
}
&lt;/pre&gt;

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On  Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

 AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

 SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace &lt;code&gt;''DATABASE_NAME''&lt;/code&gt; with the actual name of your refbase MySQL database.

If you've choosen "utf8" upon installation, then you have to make sure that variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

 &lt;meta http-equiv="content-type" content="text/html; charset=UTF-8"&gt;

In case of a latin1-based refbase installation, the contents of the &lt;code&gt;charset&lt;/code&gt; attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View &gt; Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_Portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]</text>
    <sha1>cc32c1b4a8cd9eeb57641878092b4ff895692b66</sha1>
  </revision>
  <revision>
    <id>97</id>
    <parentid>96</parentid>
    <timestamp>2023-11-05T22:09:07Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update link to Community_portal page</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14467" xml:space="preserve">This document presents solutions &amp; tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that &lt;code&gt;safe_mode&lt;/code&gt; is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
 error_reporting  =  E_ALL
 display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue. 
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the &lt;code&gt;phpinfo()&lt;/code&gt; function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; in your active ''php.ini'' file. The values given for &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [http://xampp.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

 upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

 upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [http://xampp.org/ XAMPP] the needed PHP function &lt;code&gt;iconv&lt;/code&gt; is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for &lt;code&gt;iconv&lt;/code&gt; and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.  

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table.  The &lt;code&gt;depends_path&lt;/code&gt; for the &lt;code&gt;bibutils&lt;/code&gt; record should '''not''' be &lt;code&gt;NULL&lt;/code&gt; as seen below:  

&lt;pre&gt;
mysql&gt; SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
|          1 | refbase          | true            | NULL         |
|          2 | bibutils         | true            | NULL         |
+------------+------------------+-----------------+--------------+
&lt;/pre&gt;

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;
* the PHP temp/session directory must be accessible &amp; writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable &lt;code&gt;$sessionTempDir&lt;/code&gt; in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3631
 
 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

 There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experience on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:  

&lt;pre&gt;
if (!function_exists('iconv') &amp;&amp; function_exists('libiconv')) {
   function iconv($input_encoding, $output_encoding, $string) {
       return libiconv($input_encoding, $output_encoding, $string);
   }
}
&lt;/pre&gt;

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On  Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

 AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

 SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace &lt;code&gt;''DATABASE_NAME''&lt;/code&gt; with the actual name of your refbase MySQL database.

If you've choosen "utf8" upon installation, then you have to make sure that variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

 &lt;meta http-equiv="content-type" content="text/html; charset=UTF-8"&gt;

In case of a latin1-based refbase installation, the contents of the &lt;code&gt;charset&lt;/code&gt; attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View &gt; Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]</text>
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  </revision>
  <revision>
    <id>98</id>
    <parentid>97</parentid>
    <timestamp>2023-11-05T22:10:04Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14485" xml:space="preserve">This document presents solutions &amp; tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that &lt;code&gt;safe_mode&lt;/code&gt; is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
 error_reporting  =  E_ALL
 display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue. 
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the &lt;code&gt;phpinfo()&lt;/code&gt; function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; in your active ''php.ini'' file. The values given for &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [http://xampp.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

 upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

 upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [http://xampp.org/ XAMPP] the needed PHP function &lt;code&gt;iconv&lt;/code&gt; is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for &lt;code&gt;iconv&lt;/code&gt; and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.  

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table.  The &lt;code&gt;depends_path&lt;/code&gt; for the &lt;code&gt;bibutils&lt;/code&gt; record should '''not''' be &lt;code&gt;NULL&lt;/code&gt; as seen below:  

&lt;pre&gt;
mysql&gt; SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
|          1 | refbase          | true            | NULL         |
|          2 | bibutils         | true            | NULL         |
+------------+------------------+-----------------+--------------+
&lt;/pre&gt;

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;
* the PHP temp/session directory must be accessible &amp; writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable &lt;code&gt;$sessionTempDir&lt;/code&gt; in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3631
 
 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

 There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experience on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:  

&lt;pre&gt;
if (!function_exists('iconv') &amp;&amp; function_exists('libiconv')) {
   function iconv($input_encoding, $output_encoding, $string) {
       return libiconv($input_encoding, $output_encoding, $string);
   }
}
&lt;/pre&gt;

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On  Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

 AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

 SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace &lt;code&gt;''DATABASE_NAME''&lt;/code&gt; with the actual name of your refbase MySQL database.

If you've choosen "utf8" upon installation, then you have to make sure that variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

 &lt;meta http-equiv="content-type" content="text/html; charset=UTF-8"&gt;

In case of a latin1-based refbase installation, the contents of the &lt;code&gt;charset&lt;/code&gt; attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View &gt; Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
__NOEDITSECTION__</text>
    <sha1>4b0534b2533b4c4e2aa6a23d160bcca7e6c99ce8</sha1>
  </revision>
  <revision>
    <id>99</id>
    <parentid>98</parentid>
    <timestamp>2023-11-05T22:16:46Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14511" xml:space="preserve">This document presents solutions &amp; tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that &lt;code&gt;safe_mode&lt;/code&gt; is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
 error_reporting  =  E_ALL
 display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue. 
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the &lt;code&gt;phpinfo()&lt;/code&gt; function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; in your active ''php.ini'' file. The values given for &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

 upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

 upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function &lt;code&gt;iconv&lt;/code&gt; is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for &lt;code&gt;iconv&lt;/code&gt; and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.  

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table.  The &lt;code&gt;depends_path&lt;/code&gt; for the &lt;code&gt;bibutils&lt;/code&gt; record should '''not''' be &lt;code&gt;NULL&lt;/code&gt; as seen below:  

&lt;pre&gt;
mysql&gt; SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
|          1 | refbase          | true            | NULL         |
|          2 | bibutils         | true            | NULL         |
+------------+------------------+-----------------+--------------+
&lt;/pre&gt;

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;
* the PHP temp/session directory must be accessible &amp; writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable &lt;code&gt;$sessionTempDir&lt;/code&gt; in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3631
 
 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

 There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experience on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:  

&lt;pre&gt;
if (!function_exists('iconv') &amp;&amp; function_exists('libiconv')) {
   function iconv($input_encoding, $output_encoding, $string) {
       return libiconv($input_encoding, $output_encoding, $string);
   }
}
&lt;/pre&gt;

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On  Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

 AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

 SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace &lt;code&gt;''DATABASE_NAME''&lt;/code&gt; with the actual name of your refbase MySQL database.

If you've choosen "utf8" upon installation, then you have to make sure that variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

 &lt;meta http-equiv="content-type" content="text/html; charset=UTF-8"&gt;

In case of a latin1-based refbase installation, the contents of the &lt;code&gt;charset&lt;/code&gt; attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View &gt; Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
__NOEDITSECTION__</text>
    <sha1>db3a8ad3baa2e22acc3b46df8e9150d0a0dad257</sha1>
  </revision>
  <revision>
    <id>100</id>
    <parentid>99</parentid>
    <timestamp>2023-11-05T22:27:31Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Fixed some typos</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14511" xml:space="preserve">This document presents solutions &amp; tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that &lt;code&gt;safe_mode&lt;/code&gt; is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
 error_reporting  =  E_ALL
 display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue. 
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the &lt;code&gt;phpinfo()&lt;/code&gt; function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; in your active ''php.ini'' file. The values given for &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

 upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

 upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function &lt;code&gt;iconv&lt;/code&gt; is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for &lt;code&gt;iconv&lt;/code&gt; and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.  

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table.  The &lt;code&gt;depends_path&lt;/code&gt; for the &lt;code&gt;bibutils&lt;/code&gt; record should '''not''' be &lt;code&gt;NULL&lt;/code&gt; as seen below:  

&lt;pre&gt;
mysql&gt; SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
|          1 | refbase          | true            | NULL         |
|          2 | bibutils         | true            | NULL         |
+------------+------------------+-----------------+--------------+
&lt;/pre&gt;

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;
* the PHP temp/session directory must be accessible &amp; writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable &lt;code&gt;$sessionTempDir&lt;/code&gt; in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3631
 
 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

 There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experienced on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:  

&lt;pre&gt;
if (!function_exists('iconv') &amp;&amp; function_exists('libiconv')) {
   function iconv($input_encoding, $output_encoding, $string) {
       return libiconv($input_encoding, $output_encoding, $string);
   }
}
&lt;/pre&gt;

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On  Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

 AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

 SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace &lt;code&gt;''DATABASE_NAME''&lt;/code&gt; with the actual name of your refbase MySQL database.

If you've chosen "utf8" upon installation, then you have to make sure that variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

 &lt;meta http-equiv="content-type" content="text/html; charset=UTF-8"&gt;

In case of a latin1-based refbase installation, the contents of the &lt;code&gt;charset&lt;/code&gt; attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as ·ÈÌ‡ËÏ or ÂÊ¯ˆ‰¸ etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View &gt; Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
__NOEDITSECTION__</text>
    <sha1>c17c53de38f1f1fcd858b7697dc009289e3fa8b8</sha1>
  </revision>
</page>
<page arvcontinue="20231026120622|54">
  <title>Creating the first user</title>
  <ns>0</ns>
  <id>31</id>
  <revision>
    <id>101</id>
    <timestamp>2023-11-05T22:29:36Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 09-Feb-2009</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2113" xml:space="preserve">After your (hopefully) successfull installation of refbase, you should create your own admin account.

Please, make sure that you exactly follow the steps outlined on the welcome page after successful installation. These steps are:

* Goto the main refbase page (''Home'')
* Login with email address = ''user@refbase.net'' and password = ''start''
: (make sure that the top right corner of your screen says: "You're logged in as Admin (''user@refbase.net''), if not see [[#Troubleshooting| Troubleshooting]] below)
* Click on ''Add User'' and enter the name, institutional abbreviation, email address and password of the admin user
* Open the file ''initialize/ini.inc.php'' in a text editor and change the value of the ''$adminLoginEmail'' variable to the email address you've specified for the admin user
* Log out, then login again using the email address and password of your newly created admin account

Especially note that you must set the value of the ''$adminLoginEmail'' variable in file ''initialize/ini.inc.php'' to the email address of your newly created admin user (step 4.).

== Troubleshooting ==

When being logged in as admin, you should see a red "Admin" label in front of your email address at the top right corner of the screen. An example screenshot is given [[Manual_installation#2.5_Setup_your_own_admin_user|here]]. If this is not the case for you, the following tips may help you to get things working properly.

You won't be able to login as admin using email address = ''user@refbase.net'' and password = ''start'' if you've already changed the value of the ''$adminLoginEmail'' variable ''before'' attempting to login for the first time. This variable must only be changed ''after'' you've created your own admin user.

Also, please make sure that:

* your PHP installation supports sessions
* &lt;code&gt;session.use_cookies&lt;/code&gt; is set to ON in your [[Required_PHP-INI_Settings#How_to_locate_your_active_php.ini_file|active ''php.ini'' file]]
* you have cookies enabled in your browser
* you've instructed your browser to accept cookies from your refbase site

[[Category:Installation]]</text>
    <sha1>4a44c32037f866a28ee8a9e9174670f2d1b9cdb4</sha1>
  </revision>
  <revision>
    <id>102</id>
    <parentid>101</parentid>
    <timestamp>2023-11-05T22:30:22Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2131" xml:space="preserve">After your (hopefully) successfull installation of refbase, you should create your own admin account.

Please, make sure that you exactly follow the steps outlined on the welcome page after successful installation. These steps are:

* Goto the main refbase page (''Home'')
* Login with email address = ''user@refbase.net'' and password = ''start''
: (make sure that the top right corner of your screen says: "You're logged in as Admin (''user@refbase.net''), if not see [[#Troubleshooting| Troubleshooting]] below)
* Click on ''Add User'' and enter the name, institutional abbreviation, email address and password of the admin user
* Open the file ''initialize/ini.inc.php'' in a text editor and change the value of the ''$adminLoginEmail'' variable to the email address you've specified for the admin user
* Log out, then login again using the email address and password of your newly created admin account

Especially note that you must set the value of the ''$adminLoginEmail'' variable in file ''initialize/ini.inc.php'' to the email address of your newly created admin user (step 4.).

== Troubleshooting ==

When being logged in as admin, you should see a red "Admin" label in front of your email address at the top right corner of the screen. An example screenshot is given [[Manual_installation#2.5_Setup_your_own_admin_user|here]]. If this is not the case for you, the following tips may help you to get things working properly.

You won't be able to login as admin using email address = ''user@refbase.net'' and password = ''start'' if you've already changed the value of the ''$adminLoginEmail'' variable ''before'' attempting to login for the first time. This variable must only be changed ''after'' you've created your own admin user.

Also, please make sure that:

* your PHP installation supports sessions
* &lt;code&gt;session.use_cookies&lt;/code&gt; is set to ON in your [[Required_PHP-INI_Settings#How_to_locate_your_active_php.ini_file|active ''php.ini'' file]]
* you have cookies enabled in your browser
* you've instructed your browser to accept cookies from your refbase site

[[Category:Installation]]
__NOEDITSECTION__</text>
    <sha1>8bb2a761278ef86bb8bcdab4f40340ab7c6c1f1b</sha1>
  </revision>
  <revision>
    <id>103</id>
    <parentid>102</parentid>
    <timestamp>2023-11-05T22:37:57Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Make the first list into an ordered list</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2132" xml:space="preserve">After your (hopefully) successfull installation of refbase, you should create your own admin account.

Please, make sure that you exactly follow the steps outlined on the welcome page after successful installation. These steps are:

# Goto the main refbase page (''Home'')
# Login with email address = ''user@refbase.net'' and password = ''start''
#: (make sure that the top right corner of your screen says: "You're logged in as Admin (''user@refbase.net''), if not see [[#Troubleshooting| Troubleshooting]] below)
# Click on ''Add User'' and enter the name, institutional abbreviation, email address and password of the admin user
# Open the file ''initialize/ini.inc.php'' in a text editor and change the value of the ''$adminLoginEmail'' variable to the email address you've specified for the admin user
# Log out, then login again using the email address and password of your newly created admin account

Especially note that you must set the value of the ''$adminLoginEmail'' variable in file ''initialize/ini.inc.php'' to the email address of your newly created admin user (step 4.).

== Troubleshooting ==

When being logged in as admin, you should see a red "Admin" label in front of your email address at the top right corner of the screen. An example screenshot is given [[Manual_installation#2.5_Setup_your_own_admin_user|here]]. If this is not the case for you, the following tips may help you to get things working properly.

You won't be able to login as admin using email address = ''user@refbase.net'' and password = ''start'' if you've already changed the value of the ''$adminLoginEmail'' variable ''before'' attempting to login for the first time. This variable must only be changed ''after'' you've created your own admin user.

Also, please make sure that:

* your PHP installation supports sessions
* &lt;code&gt;session.use_cookies&lt;/code&gt; is set to ON in your [[Required_PHP-INI_Settings#How_to_locate_your_active_php.ini_file|active ''php.ini'' file]]
* you have cookies enabled in your browser
* you've instructed your browser to accept cookies from your refbase site

[[Category:Installation]]
__NOEDITSECTION__</text>
    <sha1>24cd4a8a8bd45d9c5147114edfd32980264fee2e</sha1>
  </revision>
</page>
<page arvcontinue="20231106215615|104">
  <title>Release notes</title>
  <ns>0</ns>
  <id>32</id>
  <revision>
    <id>104</id>
    <timestamp>2023-11-06T21:56:15Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 23-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12774" xml:space="preserve">This document lists the major additions, changes and fixes since the release of refbase-0.9.0. See also the 'NEWS' file that comes with the refbase package.

== refbase-0.9.5 ==

=== Feature additions ===

==== Import/Add Records ====

* Added support for resource types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software

* Added import capabilities from SciFinder and Endnote XML

* refbase now supports direct import from [http://arxiv.org/ arXiv.org] &amp; [http://crossref.org/ CrossRef.org]: enter one or more arXiv IDs, DOIs or OpenURLs, and refbase will fetch &amp; import the corresponding record metadata

* Added support for direct upload of references from [http://www.sonnysoftware.com/ Bookends]

==== Export/Citation ====

* Added support for new export formats: ADS, Atom XML, ISI Web of Science, OAI_DC XML, SRW_DC XML, and Word XML

* Added new citation styles: AMA, APA, Chicago, Harvard (3 variants), MLA, and Vancouver

* refbase can now output citations in LaTeX bibliography (.bbl) format

* It is now possible to cite, group, or export ALL found records (instead of only the selected records)

* When outputting citations as PDF, US letter is now supported as page format

* Headers can now be added to cite formats via the &lt;code&gt;headerMsg&lt;/code&gt; URL parameter

* Links to corresponding files are now included in the export data if the export format and user permissions allow so

==== Search/Display ====

* refbase sports a refined interface:
** Revamped the refbase main page: all forms are now styled via CSS, and citations of the most recent publications are now dynamically included upon page load
** Redesigned the page footer &amp; header as well as the forms on the results pages
** The "Quick Search" form is now always available in the page header
** refbase now makes use of the [http://www.prototypejs.org/ Prototype] &amp; [http://script.aculo.us/ script.aculo.us] JavaScript frameworks to offer auto-completions (or search suggestions) for text entered by the user in text entry fields of the refbase interface
** Forms on search results pages can now be hidden (and if enabled by the admin, a sliding effect is now used when a user toggles the display of these forms)
** Search results can be browsed &amp; searched in three different views: List view, Citations, and Details
** Additional record info (keywords, abstract, etc) and links to cite/export the record can now be displayed underneath each citation

* refbase now supports [[OpenSearch service|OpenSearch]] which allows clients to search refbase and retrieve results in a standardized manner; as an example, this enables Firefox 3 &amp; IE 8 users to search refbase directly from their browser's toolbar, and the browsers can now offer search suggestions for search terms entered in the browser's search box

* Initial support for searching &amp; managing of duplicate records

* For the current session, refbase now offers a query history with links to any previous search results

* The ''show.php'' API now allows to include results from a refbase server into other web pages; this makes it possible to [[Integrating_refbase_into_your_web_site|dynamically include results]] from a refbase database into static HTML pages (using an &lt;code&gt;iframe&lt;/code&gt; or AJAX-style JavaScript)

* Added a "main fields" search option to the "Quick Search" form which allows to search all of the main fields at once; the list of "main fields" can be specified globally as well as individually for each user

* The default number of records per page can now be specified globally as well as individually for each user

* Added initial support for output to mobile devices (&lt;code&gt;viewType=Mobile&lt;/code&gt;)

* Many more minor enhancements

==== Localization ====

* Added initial support for spanish and [[Chinese_localization_package|chinese]] localizations

==== Command Line Clients ====

* The [[Command_line_clients|'refbase' command line client]] now supports the new export formats ''atom'', ''isi'', ''oai_dc'', ''srw_dc'' and ''word'' as well as &lt;code&gt;--view=Mobile&lt;/code&gt; and &lt;code&gt;--order=creation-date&lt;/code&gt;

* [[Command_line_clients|'refbase' command line client]]: added options &lt;code&gt;-A|--append&lt;/code&gt; and &lt;code&gt;-B|--update&lt;/code&gt; which let you append found records to a local BibTeX or MODS/SRW XML file (if they don't yet exist in that file), and update existing records in that file if their modification date on the server is more recent; by default, a backup file is created before adding or changing anything in the local file

* [[Command_line_clients|'refbase' command line client]]: added &lt;code&gt;-E|--extract&lt;/code&gt; option which extracts citation IDs from a file and retrieves matching records from refbase (supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, and (MODS|SRW|Endnote) .xml)

==== Miscellaneous ====

* Added a [http://www.mediawiki.org/wiki/Extension:Refbase refbase extension for MediaWiki] which allows to place a serial number within &lt;code&gt;&amp;lt;refbase&amp;gt;...&amp;lt;/refbase&amp;gt;&lt;/code&gt; markup tags; metadata for the reference is retrieved from refbase and marked-up according to a MediaWiki citation template

* Added support for the [http://www.sitemaps.org sitemaps.org] protocol which allows for better indexing by search engines

* The refbase [[UnAPI_service|unAPI service]] now supports the new export formats ''atom'', ''oai_dc'' and ''srw_dc''

* Many more minor enhancements

=== Changes ===

* Introduced measures to better prevent cross-site scripting (XSS) attacks

* For security reasons, HTML tags are now stripped from the &lt;code&gt;headerMsg&lt;/code&gt; URL parameter; string formatting can now be done using the refbase markup syntax

* Improved support for PHP installations running with &lt;code&gt;safe_mode=On&lt;/code&gt;

* By default, export of data via the refbase GUI is now enabled for anonymous users

* The citation output options (previously located in the results footer) have been moved to the Display Options form of the results header in Citation view

* refbase now remembers many more search &amp; display options while navigating or refining the results list

* Changed the HTTP transfer method in most forms from POST to GET; this helps to avoid warnings about re-sending POST data in some browsers (such as Firefox)

* We now use a ''show.php'' URL for the "show details" link in the search results list since it is much shorter and easier to bookmark as a permanent link

* When linking to particular records via ''show.php'', one can now use consecutive serial number ranges as values of the &lt;code&gt;records&lt;/code&gt; parameter; examples: ''show.php?records=123-131'' or ''show.php?records=123-141,145,147,150-152''

* When viewing/outputting citations, the list of citations can now be sorted by record creation date (use &lt;code&gt;citeOrder=creation-date&lt;/code&gt; in ''show.php'' URLs); this allows to sort records such that newly added/edited records get listed top of the list

* Redesigned the page footer to make it fit on one line (and thus less heavy)

* Added many CSS attributes (id/class names) to HTML output where appropriate; this allows to easier refine the CSS styling of the refbase interface

* The admin can now define any of the supported views (List view, Citations, Details) as the default view

* For each view, the admin can now define whether the results header &amp; footer should be displayed open or closed by default, or whether they should be entirely hidden from the interface

* The admin can now customize the list of fields that are displayed by default in List &amp; Details view; similarly, the list of fields that are available in dropdown menus of the results header can also be customized

* The admin can now define ''accesskey'' values which allow for keyboard navigation of the main parts of the refbase interface

* The &lt;code&gt;$databaseBaseURL&lt;/code&gt; in ''ini.inc.php'' is now auto-generated by default

* The refbase logo image files have been updated to the new refbase logo, and the logo URL path &amp; dimensions can now be customized easily via ''ini.inc.php''

* The session/temp dir path can now be specified explicitly in ''ini.inc.php''; this allows you to define a custom directory path that's used on your server to save session data and to write any temporary files

* The ''edition'' field now accepts string values

* After any add, edit, or delete action, refbase now includes a link to the last multi-record search result list in the feedback header message if the previous query resulted in a single record; together with other changes, this obviates ''receipt.php''

* By default, the SRU formats ''SRW_DC XML'' and ''SRW_MODS XML'' are now transformed to HTML via XSL stylesheets

* Authenticated users can now use ''opensearch.php'' or ''sru.php'' to query any of their user-specific fields

* For OpenSearch &amp; SRU searches, the ''keywords'' field will now be queried by default if no context set &amp; index name is given ("cql.serverChoice")

* Renamed the [[Bibutils]] ''xml2word'' command line tool to ''xml2wordbib'' according to the name changes in Bibutils v3.40; note that if you're using a Bibutils version prior to Bibutils v3.40, you must revert this change in file ''export/bibutils/export_xml2word.php''

* Underline fontshape markup is now supported in various import and citation formats as well as in refbase markup (use: &lt;code&gt;__underlined text__&lt;/code&gt;)

* When importing multiple records, ALL records are now imported by default

* Improved UTF-8 handling on import so that e.g. a best-effort conversion is done for UTF-8 data which are imported into a latin1-based database

* When importing (or exporting) RIS records, the type of thesis (such as "Masters thesis" or "Ph.D. thesis") is now taken from (or exported to) the ''U1'' field (as is supported by Bibutils v3.35 or greater);

* Upon import, if the given URL actually is a DOI prefixed with [http://dx.doi.org/ http://dx.doi.org/], we'll extract the DOI and move it to the ''doi'' field

* Import of user-specific fields into the "Add record" form is now possible

* We now generate (or honour existing) cite keys/IDs for the import data, and copy them to the user's ''cite_key'' field; the uniqueness of cite keys is ensured among all imported records as well as the user's existing records

* Improved recognition of PubMed resource types

* For the "Extract citations" functionality, we now check whether the extracted serial numbers and cite keys exist in the database and report any missing record identifiers

* Changed or merged some localization strings to allow for better translations to languages such as Spanish or Chinese

* Refined layout of ''user_receipt.php''

* The [[Command_line_clients#.27refbase_import.27_command_line_client|'refbase_import' command line client]] now supports common output options from the 'refbase' CLI client; this allows to instruct the refbase server to return all imported records in any of the supported export or citation formats &amp; styles

* Many more minor changes

=== Bug fixes ===

* Fixed bug that prevented correct directory creation/renaming and/or file upload on some platforms

* Fixed &lt;code&gt;preg_match()&lt;/code&gt; compilation errors when importing BibTeX records into a refbase UTF-8 database

* When importing PubMed MEDLINE source data, we now extract author information from the ''AU'' field if the ''FAU'' field is not available

* We now convert Endnote XML text style markup into appropriate refbase markup

* Upon RIS import, we now make sure that HTML encoded source data (such as &lt;code&gt;&amp;amp;auml;&lt;/code&gt;, &lt;code&gt;&amp;amp;#xF6;&lt;/code&gt; or &lt;code&gt;&amp;amp;#233;&lt;/code&gt;) get decoded before import

* Records of unrecognized resource type were omitted upon citation output; fixed

* When outputting to LaTeX or RIS, curly brackets are now escaped to avoid incorrect output

* Fixed an issue were it wasn't possible to correctly import (or cite) records which contained non-ASCII characters in author's given names

* Worked around an error in Internet Explorer when importing single records via the web interface

* Fixed an error when exporting data to ODF XML and when the user-specific fields were missing from the SQL query

* Fixed referrer-related problems that could cause unexpected behaviour and incorrect warning/error messages; however note that working simultaneously in different browser windows or tabs can still cause some unexpected results

* Worked around PREG compilation errors on some UTF8-based systems

* For theses, the corporate author (i.e. the corporate body granting the degree) is now labeled correctly in MODS XML output; as a result, the degree grantor is now recognized correctly by Bibutils and copied to the BibTeX ''school'' field

* Many more minor bug fixes

[[Category:General]]</text>
    <sha1>899926c4a3a3580d324785268cdc789328f81ca3</sha1>
  </revision>
  <revision>
    <id>105</id>
    <parentid>104</parentid>
    <timestamp>2023-11-06T21:56:46Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="12792" xml:space="preserve">This document lists the major additions, changes and fixes since the release of refbase-0.9.0. See also the 'NEWS' file that comes with the refbase package.

== refbase-0.9.5 ==

=== Feature additions ===

==== Import/Add Records ====

* Added support for resource types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software

* Added import capabilities from SciFinder and Endnote XML

* refbase now supports direct import from [http://arxiv.org/ arXiv.org] &amp; [http://crossref.org/ CrossRef.org]: enter one or more arXiv IDs, DOIs or OpenURLs, and refbase will fetch &amp; import the corresponding record metadata

* Added support for direct upload of references from [http://www.sonnysoftware.com/ Bookends]

==== Export/Citation ====

* Added support for new export formats: ADS, Atom XML, ISI Web of Science, OAI_DC XML, SRW_DC XML, and Word XML

* Added new citation styles: AMA, APA, Chicago, Harvard (3 variants), MLA, and Vancouver

* refbase can now output citations in LaTeX bibliography (.bbl) format

* It is now possible to cite, group, or export ALL found records (instead of only the selected records)

* When outputting citations as PDF, US letter is now supported as page format

* Headers can now be added to cite formats via the &lt;code&gt;headerMsg&lt;/code&gt; URL parameter

* Links to corresponding files are now included in the export data if the export format and user permissions allow so

==== Search/Display ====

* refbase sports a refined interface:
** Revamped the refbase main page: all forms are now styled via CSS, and citations of the most recent publications are now dynamically included upon page load
** Redesigned the page footer &amp; header as well as the forms on the results pages
** The "Quick Search" form is now always available in the page header
** refbase now makes use of the [http://www.prototypejs.org/ Prototype] &amp; [http://script.aculo.us/ script.aculo.us] JavaScript frameworks to offer auto-completions (or search suggestions) for text entered by the user in text entry fields of the refbase interface
** Forms on search results pages can now be hidden (and if enabled by the admin, a sliding effect is now used when a user toggles the display of these forms)
** Search results can be browsed &amp; searched in three different views: List view, Citations, and Details
** Additional record info (keywords, abstract, etc) and links to cite/export the record can now be displayed underneath each citation

* refbase now supports [[OpenSearch service|OpenSearch]] which allows clients to search refbase and retrieve results in a standardized manner; as an example, this enables Firefox 3 &amp; IE 8 users to search refbase directly from their browser's toolbar, and the browsers can now offer search suggestions for search terms entered in the browser's search box

* Initial support for searching &amp; managing of duplicate records

* For the current session, refbase now offers a query history with links to any previous search results

* The ''show.php'' API now allows to include results from a refbase server into other web pages; this makes it possible to [[Integrating_refbase_into_your_web_site|dynamically include results]] from a refbase database into static HTML pages (using an &lt;code&gt;iframe&lt;/code&gt; or AJAX-style JavaScript)

* Added a "main fields" search option to the "Quick Search" form which allows to search all of the main fields at once; the list of "main fields" can be specified globally as well as individually for each user

* The default number of records per page can now be specified globally as well as individually for each user

* Added initial support for output to mobile devices (&lt;code&gt;viewType=Mobile&lt;/code&gt;)

* Many more minor enhancements

==== Localization ====

* Added initial support for spanish and [[Chinese_localization_package|chinese]] localizations

==== Command Line Clients ====

* The [[Command_line_clients|'refbase' command line client]] now supports the new export formats ''atom'', ''isi'', ''oai_dc'', ''srw_dc'' and ''word'' as well as &lt;code&gt;--view=Mobile&lt;/code&gt; and &lt;code&gt;--order=creation-date&lt;/code&gt;

* [[Command_line_clients|'refbase' command line client]]: added options &lt;code&gt;-A|--append&lt;/code&gt; and &lt;code&gt;-B|--update&lt;/code&gt; which let you append found records to a local BibTeX or MODS/SRW XML file (if they don't yet exist in that file), and update existing records in that file if their modification date on the server is more recent; by default, a backup file is created before adding or changing anything in the local file

* [[Command_line_clients|'refbase' command line client]]: added &lt;code&gt;-E|--extract&lt;/code&gt; option which extracts citation IDs from a file and retrieves matching records from refbase (supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, and (MODS|SRW|Endnote) .xml)

==== Miscellaneous ====

* Added a [http://www.mediawiki.org/wiki/Extension:Refbase refbase extension for MediaWiki] which allows to place a serial number within &lt;code&gt;&amp;lt;refbase&amp;gt;...&amp;lt;/refbase&amp;gt;&lt;/code&gt; markup tags; metadata for the reference is retrieved from refbase and marked-up according to a MediaWiki citation template

* Added support for the [http://www.sitemaps.org sitemaps.org] protocol which allows for better indexing by search engines

* The refbase [[UnAPI_service|unAPI service]] now supports the new export formats ''atom'', ''oai_dc'' and ''srw_dc''

* Many more minor enhancements

=== Changes ===

* Introduced measures to better prevent cross-site scripting (XSS) attacks

* For security reasons, HTML tags are now stripped from the &lt;code&gt;headerMsg&lt;/code&gt; URL parameter; string formatting can now be done using the refbase markup syntax

* Improved support for PHP installations running with &lt;code&gt;safe_mode=On&lt;/code&gt;

* By default, export of data via the refbase GUI is now enabled for anonymous users

* The citation output options (previously located in the results footer) have been moved to the Display Options form of the results header in Citation view

* refbase now remembers many more search &amp; display options while navigating or refining the results list

* Changed the HTTP transfer method in most forms from POST to GET; this helps to avoid warnings about re-sending POST data in some browsers (such as Firefox)

* We now use a ''show.php'' URL for the "show details" link in the search results list since it is much shorter and easier to bookmark as a permanent link

* When linking to particular records via ''show.php'', one can now use consecutive serial number ranges as values of the &lt;code&gt;records&lt;/code&gt; parameter; examples: ''show.php?records=123-131'' or ''show.php?records=123-141,145,147,150-152''

* When viewing/outputting citations, the list of citations can now be sorted by record creation date (use &lt;code&gt;citeOrder=creation-date&lt;/code&gt; in ''show.php'' URLs); this allows to sort records such that newly added/edited records get listed top of the list

* Redesigned the page footer to make it fit on one line (and thus less heavy)

* Added many CSS attributes (id/class names) to HTML output where appropriate; this allows to easier refine the CSS styling of the refbase interface

* The admin can now define any of the supported views (List view, Citations, Details) as the default view

* For each view, the admin can now define whether the results header &amp; footer should be displayed open or closed by default, or whether they should be entirely hidden from the interface

* The admin can now customize the list of fields that are displayed by default in List &amp; Details view; similarly, the list of fields that are available in dropdown menus of the results header can also be customized

* The admin can now define ''accesskey'' values which allow for keyboard navigation of the main parts of the refbase interface

* The &lt;code&gt;$databaseBaseURL&lt;/code&gt; in ''ini.inc.php'' is now auto-generated by default

* The refbase logo image files have been updated to the new refbase logo, and the logo URL path &amp; dimensions can now be customized easily via ''ini.inc.php''

* The session/temp dir path can now be specified explicitly in ''ini.inc.php''; this allows you to define a custom directory path that's used on your server to save session data and to write any temporary files

* The ''edition'' field now accepts string values

* After any add, edit, or delete action, refbase now includes a link to the last multi-record search result list in the feedback header message if the previous query resulted in a single record; together with other changes, this obviates ''receipt.php''

* By default, the SRU formats ''SRW_DC XML'' and ''SRW_MODS XML'' are now transformed to HTML via XSL stylesheets

* Authenticated users can now use ''opensearch.php'' or ''sru.php'' to query any of their user-specific fields

* For OpenSearch &amp; SRU searches, the ''keywords'' field will now be queried by default if no context set &amp; index name is given ("cql.serverChoice")

* Renamed the [[Bibutils]] ''xml2word'' command line tool to ''xml2wordbib'' according to the name changes in Bibutils v3.40; note that if you're using a Bibutils version prior to Bibutils v3.40, you must revert this change in file ''export/bibutils/export_xml2word.php''

* Underline fontshape markup is now supported in various import and citation formats as well as in refbase markup (use: &lt;code&gt;__underlined text__&lt;/code&gt;)

* When importing multiple records, ALL records are now imported by default

* Improved UTF-8 handling on import so that e.g. a best-effort conversion is done for UTF-8 data which are imported into a latin1-based database

* When importing (or exporting) RIS records, the type of thesis (such as "Masters thesis" or "Ph.D. thesis") is now taken from (or exported to) the ''U1'' field (as is supported by Bibutils v3.35 or greater);

* Upon import, if the given URL actually is a DOI prefixed with [http://dx.doi.org/ http://dx.doi.org/], we'll extract the DOI and move it to the ''doi'' field

* Import of user-specific fields into the "Add record" form is now possible

* We now generate (or honour existing) cite keys/IDs for the import data, and copy them to the user's ''cite_key'' field; the uniqueness of cite keys is ensured among all imported records as well as the user's existing records

* Improved recognition of PubMed resource types

* For the "Extract citations" functionality, we now check whether the extracted serial numbers and cite keys exist in the database and report any missing record identifiers

* Changed or merged some localization strings to allow for better translations to languages such as Spanish or Chinese

* Refined layout of ''user_receipt.php''

* The [[Command_line_clients#.27refbase_import.27_command_line_client|'refbase_import' command line client]] now supports common output options from the 'refbase' CLI client; this allows to instruct the refbase server to return all imported records in any of the supported export or citation formats &amp; styles

* Many more minor changes

=== Bug fixes ===

* Fixed bug that prevented correct directory creation/renaming and/or file upload on some platforms

* Fixed &lt;code&gt;preg_match()&lt;/code&gt; compilation errors when importing BibTeX records into a refbase UTF-8 database

* When importing PubMed MEDLINE source data, we now extract author information from the ''AU'' field if the ''FAU'' field is not available

* We now convert Endnote XML text style markup into appropriate refbase markup

* Upon RIS import, we now make sure that HTML encoded source data (such as &lt;code&gt;&amp;amp;auml;&lt;/code&gt;, &lt;code&gt;&amp;amp;#xF6;&lt;/code&gt; or &lt;code&gt;&amp;amp;#233;&lt;/code&gt;) get decoded before import

* Records of unrecognized resource type were omitted upon citation output; fixed

* When outputting to LaTeX or RIS, curly brackets are now escaped to avoid incorrect output

* Fixed an issue were it wasn't possible to correctly import (or cite) records which contained non-ASCII characters in author's given names

* Worked around an error in Internet Explorer when importing single records via the web interface

* Fixed an error when exporting data to ODF XML and when the user-specific fields were missing from the SQL query

* Fixed referrer-related problems that could cause unexpected behaviour and incorrect warning/error messages; however note that working simultaneously in different browser windows or tabs can still cause some unexpected results

* Worked around PREG compilation errors on some UTF8-based systems

* For theses, the corporate author (i.e. the corporate body granting the degree) is now labeled correctly in MODS XML output; as a result, the degree grantor is now recognized correctly by Bibutils and copied to the BibTeX ''school'' field

* Many more minor bug fixes

[[Category:General]]
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</page>
<page arvcontinue="20231106215615|104">
  <title>The 'next release' question</title>
  <ns>0</ns>
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    <comment>Original page content from 09-Dec-2006</comment>
    <model>wikitext</model>
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    <text bytes="776" xml:space="preserve">Often, the question arises: ''When do you release the next version of refbase?''

It is not easy to give an answer to that question. Unfortunately, we cannot (and don't want to) announce exact release dates. Experience shows that these dates are almost never met and it only leads to user frustration. We understand that it may seem equally frustrating that there is no info at all. But this is as good as we can do.

Nevertheless, refbase is under constant development. The most recent fixes &amp; additions are available in our [[SVN_version|SVN repository]].

We encourage you to leave your ideas for future enhancements at the [[Feature request]] page in the wiki or in our [http://sourceforge.net/forum/forum.php?forum_id=351913 Feature Requests forum].

[[Category:General]]</text>
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      <id>1</id>
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    <minor/>
    <comment>Update link to refbase Feature Requests forum</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="774" xml:space="preserve">Often, the question arises: ''When do you release the next version of refbase?''

It is not easy to give an answer to that question. Unfortunately, we cannot (and don't want to) announce exact release dates. Experience shows that these dates are almost never met and it only leads to user frustration. We understand that it may seem equally frustrating that there is no info at all. But this is as good as we can do.

Nevertheless, refbase is under constant development. The most recent fixes &amp; additions are available in our [[SVN_version|SVN repository]].

We encourage you to leave your ideas for future enhancements at the [[Feature request]] page in the wiki or in our [https://sourceforge.net/p/refbase/discussion/351913/ Feature Requests forum].

[[Category:General]]</text>
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</page>
<page arvcontinue="20231106215615|104">
  <title>Roadmap</title>
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    </contributor>
    <comment>Original page content from 20-Nov-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="490" xml:space="preserve">This is a rough roadmap of feature additions and bug fixes for our upcoming releases.

== Post refbase-0.9.5 ==

* Discussion
** Coding style
** HTML layout (templates/skins, CSS styling)
** Reference types
** Citation formatting
** Ways to improve build/release cycle
** How to further modularize the code to allow for other RDBMS, custom database schemes and a plugin mechanism
** Prioritize [[Planned_feature_additions|planned features]]
* Fix referrer-related bugs

[[Category:General]]</text>
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    <id>109</id>
    <parentid>108</parentid>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="508" xml:space="preserve">This is a rough roadmap of feature additions and bug fixes for our upcoming releases.

== Post refbase-0.9.5 ==

* Discussion
** Coding style
** HTML layout (templates/skins, CSS styling)
** Reference types
** Citation formatting
** Ways to improve build/release cycle
** How to further modularize the code to allow for other RDBMS, custom database schemes and a plugin mechanism
** Prioritize [[Planned_feature_additions|planned features]]
* Fix referrer-related bugs

[[Category:General]]
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<page arvcontinue="20231106215615|104">
  <title>Configuring refbase</title>
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    <comment>Original page content from 09-Dec-2008</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14249" xml:space="preserve">This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable &lt;code&gt;$logoImageURL&lt;/code&gt; in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables &lt;code&gt;$logoImageWidth&lt;/code&gt; and &lt;code&gt;$logoImageHeight&lt;/code&gt; to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (&lt;code&gt;$logoSmallImageURL&lt;/code&gt; and &lt;code&gt;$faviconImageURL&lt;/code&gt;).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the &lt;code&gt;$defaultNumberOfRecords&lt;/code&gt; variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

 // The default language selection, can be overwritten by userdefined language
 $defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the &lt;code&gt;$defaultLanguage&lt;/code&gt; variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable &lt;code&gt;$fileVisibility&lt;/code&gt; in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable &lt;code&gt;$fileVisibilityException&lt;/code&gt; (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

 $fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field &amp; identifier string in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

 $fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

 $fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options &amp; permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the &lt;code&gt;userID=0&lt;/code&gt; parameter:

 user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called &lt;code&gt;$fileVisibility&lt;/code&gt;. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.
 
Additionally, you can set exceptions to this rule in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable &lt;code&gt;$defaultCiteStyle&lt;/code&gt; in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names &amp; order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

 UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables &lt;code&gt;$defaultCiteStyle&lt;/code&gt; and &lt;code&gt;$defaultUserStyles&lt;/code&gt; in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

 UPDATE styles SET order_by = "2" WHERE style_id = 1;
 UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

 UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type &lt;code&gt;varchar(25)&lt;/code&gt;, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called &lt;code&gt;citeRecord()&lt;/code&gt;. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

 INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace &lt;code&gt;STYLENAME&lt;/code&gt; with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, &lt;code&gt;STYLEFILE&lt;/code&gt; must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

 SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

 UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [http://refbase.svn.sourceforge.net/viewvc/refbase/ refbase subversion repository] for new styles that are under development but not yet included in the project release.  Be aware that styles obtained from the [http://refbase.svn.sourceforge.net/viewvc/refbase/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.  

----
Todo-list: 
*A link is set from [[Adding Records]]-page: how to configure different Types of publication and different Types of Thesis
**in the database
**in view options

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

 INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace &lt;code&gt;LANGCODE&lt;/code&gt; with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

 SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]</text>
    <sha1>b8a9202cb3858aa2a6ea24d4a2a5725e367f2bea</sha1>
  </revision>
  <revision>
    <id>111</id>
    <parentid>110</parentid>
    <timestamp>2023-11-06T22:24:16Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14267" xml:space="preserve">This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable &lt;code&gt;$logoImageURL&lt;/code&gt; in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables &lt;code&gt;$logoImageWidth&lt;/code&gt; and &lt;code&gt;$logoImageHeight&lt;/code&gt; to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (&lt;code&gt;$logoSmallImageURL&lt;/code&gt; and &lt;code&gt;$faviconImageURL&lt;/code&gt;).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the &lt;code&gt;$defaultNumberOfRecords&lt;/code&gt; variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

 // The default language selection, can be overwritten by userdefined language
 $defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the &lt;code&gt;$defaultLanguage&lt;/code&gt; variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable &lt;code&gt;$fileVisibility&lt;/code&gt; in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable &lt;code&gt;$fileVisibilityException&lt;/code&gt; (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

 $fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field &amp; identifier string in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

 $fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

 $fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options &amp; permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the &lt;code&gt;userID=0&lt;/code&gt; parameter:

 user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called &lt;code&gt;$fileVisibility&lt;/code&gt;. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.
 
Additionally, you can set exceptions to this rule in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable &lt;code&gt;$defaultCiteStyle&lt;/code&gt; in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names &amp; order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

 UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables &lt;code&gt;$defaultCiteStyle&lt;/code&gt; and &lt;code&gt;$defaultUserStyles&lt;/code&gt; in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

 UPDATE styles SET order_by = "2" WHERE style_id = 1;
 UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

 UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type &lt;code&gt;varchar(25)&lt;/code&gt;, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called &lt;code&gt;citeRecord()&lt;/code&gt;. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

 INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace &lt;code&gt;STYLENAME&lt;/code&gt; with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, &lt;code&gt;STYLEFILE&lt;/code&gt; must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

 SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

 UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [http://refbase.svn.sourceforge.net/viewvc/refbase/ refbase subversion repository] for new styles that are under development but not yet included in the project release.  Be aware that styles obtained from the [http://refbase.svn.sourceforge.net/viewvc/refbase/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.  

----
Todo-list: 
*A link is set from [[Adding Records]]-page: how to configure different Types of publication and different Types of Thesis
**in the database
**in view options

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

 INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace &lt;code&gt;LANGCODE&lt;/code&gt; with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

 SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]
__NOEDITSECTION__</text>
    <sha1>eb64f16d11de8ba75852b552bcbd88f61647f66a</sha1>
  </revision>
  <revision>
    <id>116</id>
    <parentid>111</parentid>
    <timestamp>2023-11-07T12:43:03Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14265" xml:space="preserve">This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable &lt;code&gt;$logoImageURL&lt;/code&gt; in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables &lt;code&gt;$logoImageWidth&lt;/code&gt; and &lt;code&gt;$logoImageHeight&lt;/code&gt; to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (&lt;code&gt;$logoSmallImageURL&lt;/code&gt; and &lt;code&gt;$faviconImageURL&lt;/code&gt;).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the &lt;code&gt;$defaultNumberOfRecords&lt;/code&gt; variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

 // The default language selection, can be overwritten by userdefined language
 $defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the &lt;code&gt;$defaultLanguage&lt;/code&gt; variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable &lt;code&gt;$fileVisibility&lt;/code&gt; in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable &lt;code&gt;$fileVisibilityException&lt;/code&gt; (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

 $fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field &amp; identifier string in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

 $fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

 $fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options &amp; permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the &lt;code&gt;userID=0&lt;/code&gt; parameter:

 user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called &lt;code&gt;$fileVisibility&lt;/code&gt;. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.
 
Additionally, you can set exceptions to this rule in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable &lt;code&gt;$defaultCiteStyle&lt;/code&gt; in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names &amp; order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

 UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables &lt;code&gt;$defaultCiteStyle&lt;/code&gt; and &lt;code&gt;$defaultUserStyles&lt;/code&gt; in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

 UPDATE styles SET order_by = "2" WHERE style_id = 1;
 UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

 UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type &lt;code&gt;varchar(25)&lt;/code&gt;, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called &lt;code&gt;citeRecord()&lt;/code&gt;. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

 INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace &lt;code&gt;STYLENAME&lt;/code&gt; with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, &lt;code&gt;STYLEFILE&lt;/code&gt; must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

 SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

 UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [https://sourceforge.net/p/refbase/code/HEAD/tree/ refbase subversion repository] for new styles that are under development but not yet included in the project release.  Be aware that styles obtained from the [https://sourceforge.net/p/refbase/code/HEAD/tree/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.  

----
Todo-list: 
*A link is set from [[Adding Records]]-page: how to configure different Types of publication and different Types of Thesis
**in the database
**in view options

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

 INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace &lt;code&gt;LANGCODE&lt;/code&gt; with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

 SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]
__NOEDITSECTION__</text>
    <sha1>d5637455a8cd188ed276754b777150cb762f29ab</sha1>
  </revision>
  <revision>
    <id>139</id>
    <parentid>116</parentid>
    <timestamp>2023-11-20T17:09:56Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Remove "todo comments" about configuring different publication &amp; thesis types</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14088" xml:space="preserve">This document presents some tips how to configure your refbase installation:

The refbase admin has a variety of options to configure or customize refbase. Some of them are listed in this article. If you don't find the desired option, please refer to file ''initialize/ini.inc.php'' within your refbase installation. This configuration file contains many global settings which are not accessible via the refbase web interface:

* initial database settings (database name, admin email, database URL, character set, etc)
* default user settings when a new user is created
* visibility of files (e.g., .pdf files)
* important settings for file upload (file renaming, directory creation, etc)
* appearance of links within refbase
* server settings for link resolvers (OpenURL, ISBN)
* rich text formatting (e.g., greek letters, italic or superscript/subscript text)

The configuration file ''initialize/ini.inc.php'' is well commented, therefore you will find much more information in this file.

Below you can find answers to some frequently asked questions about configuring refbase.

== How can I change the logo? ==

You can change the main logo image that's displayed in the refbase page header by setting variable &lt;code&gt;$logoImageURL&lt;/code&gt; in ''initialize/ini.inc.php'' to the path of your logo file. In addition, please be sure to set the variables &lt;code&gt;$logoImageWidth&lt;/code&gt; and &lt;code&gt;$logoImageHeight&lt;/code&gt; to the dimensions of your logo. You may also be interested to specify your own paths for the smaller logos (&lt;code&gt;$logoSmallImageURL&lt;/code&gt; and &lt;code&gt;$faviconImageURL&lt;/code&gt;).

== How can I setup refbase so that users can register themselves? ==

By default, only the admin is allowed to setup new user accounts. Here's how to setup your refbase installation such that users can automatically register themselves:

In ''initialize/ini.inc.php'' set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable to "everyone". Then, provide a link on the main page to ''user_details.php'' where users can use the provided form to register themselves.

Just set the &lt;code&gt;$addNewUsers&lt;/code&gt; variable back to "admin" if you want to prevent other users from messing with your users table.

== How can I change the default number of records shown? ==

You can change the default number of records that is returned by any (web, RSS or SRU) query by changing the value of the &lt;code&gt;$defaultNumberOfRecords&lt;/code&gt; variable in ''initialize/ini.inc.php''.

== How can I change the default language? ==

You can change the language that's displayed by default in file ''intialize/ini.inc.php'' within your refbase root directory. Search for this paragraph:

 // The default language selection, can be overwritten by userdefined language
 $defaultLanguage = "de"; // e.g. "en", "de" or "fr"

and set the value of the &lt;code&gt;$defaultLanguage&lt;/code&gt; variable to either "en" (English), "de" (German) or "fr" (French). In case of problems, please check that your desired default language is enabled within MySQL table ''languages''.

Note that logged-in database users can switch to another language. This can be done by clicking the ''Options'' link when logged in.

== How can I make some PDFs available to all users? ==

Ususally, access to PDFs should only be made available to logged-in users. This is controlled by variable &lt;code&gt;$fileVisibility&lt;/code&gt; in ''initialize/ini.inc.php''. However, often one wants to make a few PDFs available to all users. Variable &lt;code&gt;$fileVisibilityException&lt;/code&gt; (also in ''initialize/ini.inc.php'') can be used to specify a condition where attached files will be displayed to ''all'' users, no matter whether they're logged in or not.

By default, refbase will publicly display files for all records where the ''thesis'' field in table ''refs'' is not empty, i.e. if a thesis type has been specified for the record:

 $fileVisibilityException = array("thesis", "/.+/");

If, instead, you'd like to allow public access to PDFs for arbitrary records, a common approach would be to put some unique string into one of the fields from table ''refs'', and use this field &amp; identifier string in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;.†As an example, for all records where the attached PDF should be displayed publicly, you could add the string "author copyright" to the ''notes'' field. Then use the following pattern:

 $fileVisibilityException = array("notes", "/author copyright/");

As another example, if you'd like to offer public access to all PDFs that where authored by a member of your institution, you could make use of the ''contribution_id'' field ([[Auto-updating_author/group_bibliographies#Institutional_or_group_bibliographies|more info]]), and specify this field and your institutional abbreviation in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;. If your institutional abbreviation is, say, "NUCAPT", you'd use this pattern:

 $fileVisibilityException = array("contribution_id", "/NUCAPT/");

== How can I change options &amp; permissions for everyone who's not logged in? ==

=== Setting options via the web interface ===

When logged in as admin, you can set options and access permissions for everyone who's not logged in by calling the script ''user_options.php'' with the &lt;code&gt;userID=0&lt;/code&gt; parameter:

 user_options.php?userID=0

For all permissions that are set to off, the relevant interface elements will be hidden from the refbase GUI.

Note that some of the available user permissions require a user being logged in. I.e., enabling these options for anyone who isn't logged in won't have any effect. Following user permissions require a login:

* Add records
* Edit records
* Delete records
* File upload
* User groups
* User queries
* Import
* Batch import
* Modify options

If you want to allow users who are not logged in to query the refbase database via the [[Search/Retrieve web services|SRU search/retrieve webservice]], then either the ''Export'' or the ''Batch export'' user permission needs to be enabled. This will allow export of XML records via ''sru.php'' but won't allow a user who isn't logged in to export records via the web interface.

=== Setting options within ''ini.inc.php'' ===

If you like to change the permission to see/download files (e.g., .pdf files), you (the admin) can find the appropriate option in file ''initialize/ini.inc.php''. The relevant variable is called &lt;code&gt;$fileVisibility&lt;/code&gt;. You are able to allow file download for everyone, logged-in users only, or on a user-specific basis.
 
Additionally, you can set exceptions to this rule in variable &lt;code&gt;$fileVisibilityException&lt;/code&gt;, which enables you to always allow download access to files that meet a particular criterion. A typical usage example would be to always grant download access to theses or papers that were written by members of your own institution.

For more details, please refer to the comments in ''ini.inc.php''.

== How can I change the default citation style? ==

You can use variable &lt;code&gt;$defaultCiteStyle&lt;/code&gt; in file ''initialize/ini.in.php'' to change the citation style that's displayed by default in the web interface (Citation view) as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. The given style name must have a matching entry in the ''styles'' table of your refbase MySQL database.

Note that the admin can enable or disable particular citation styles individually for each user. And if desired, logged-in users can deselect some of the enabled styles in their user-specific options.

== How can I change the names &amp; order of citation styles? ==

=== Changing the names of citation styles ===

Here's how to change the names of citation styles displayed in the "Cite using style" drop-down (in the form below the query results list): Currently, you have to directly edit the ''styles'' MySQL table. E.g., to change the display name of the "Polar Biol" citation style to "Default" execute the following MySQL command from within your SQL command line interpreter:

 UPDATE styles SET style_name = "Default" WHERE style_name = "Polar Biol";

Note that you must also change the corresponding names for the variables &lt;code&gt;$defaultCiteStyle&lt;/code&gt; and &lt;code&gt;$defaultUserStyles&lt;/code&gt; in ''initialize/ini.inc.php''.

=== Changing the order of citation styles ===

Similar to the above, you can edit the ''styles'' MySQL table to change the order of citation styles displayed in the "Cite using style" drop-down menu. If, for example, you want to switch the order of the first two citation styles, execute the two commands below:

 UPDATE styles SET order_by = "2" WHERE style_id = 1;
 UPDATE styles SET order_by = "1" WHERE style_id = 2;

Note: this example assumes that you have table entries with style_id's of 1 and 2, otherwise adopt or use something like:

 UPDATE styles SET order_by = "...(whatever)..." WHERE style_name = "...(whatever)..."

The ''order_by'' field is of type &lt;code&gt;varchar(25)&lt;/code&gt;, i.e., you can also use more fine grained values (such as "1a", "1b", etc).

== How can I add or disable a particular citation style? ==

=== Adding a citation style ===

Currently, citation styles are written as a PHP function, so you'll need to know a bit of PHP to add your own style. The PHP function that outputs records in citation format is called &lt;code&gt;citeRecord()&lt;/code&gt;. For each citation style, there's a separate file with a dedictated version of this function. These citation style files are located within the ''cite'' sub-directory of your refbase root directory.

To build your own style, you may want to have a look at the existing citation style files and [[#How to create a new citation style|modify]] one of them to suit your needs.

After you've created your own citation style, copy it into the ''cite'' sub-directory of your refbase root directory. Then, in order to add your citation style file to the "Cite using style" drop-down, execute the following MySQL command from within your SQL command line interpreter:

 INSERT INTO styles VALUES (NULL, 'STYLENAME', 'true', 'STYLEFILE', '1', '1');

In the above MySQL command, replace &lt;code&gt;STYLENAME&lt;/code&gt; with the actual name of your citation style. This name will appear in the "Cite using style" drop-down. Similarly, &lt;code&gt;STYLEFILE&lt;/code&gt; must be replaced with the file name of your citation style file, prefixed with "styles/" (example: "styles/MyStyleFile.php"). In addition, you can change the first number ('1') in the above command to change the position at which your style name will be displayed in the drop-down. To see all available styles and confirm that your style has been successfully added to the ''styles'' MySQL table, execute this command:

 SELECT * FROM styles;

Now, login as admin via the refbase web interface, click on "Manage Users" and activate your new style (using the "edit options" link) for all those users who shall see this style. If you've enabled/disabled any citation styles for the admin user, you'll have to logout and login again in order to see your changes.

=== Disabling a citation style ===

You can globally disable existing styles by setting the ''style_enabled'' field to "false". E.g., if you want to disable the "Polar Biol" citation style, execute:

 UPDATE styles SET style_enabled = "false" WHERE style_name = "Polar Biol";

=== How to create a new citation style ===

Before we start this section, a comment in advance:

To improve refbase: If you have created a new citation style, we would be interested to offer this style for all refbase users. If possible, please
* post this new .php file to [[refbase:Community_Portal|the community]].
* include the journal title for you built the style with their website.

This section should contain information/hints for non-php professionals

==== Adapting existing work ====

Before investing energy in creating a new style, it is wise to check the [https://sourceforge.net/p/refbase/code/HEAD/tree/ refbase subversion repository] for new styles that are under development but not yet included in the project release.  Be aware that styles obtained from the [https://sourceforge.net/p/refbase/code/HEAD/tree/branches/bleeding-edge/cite/styles/ bleeding edge branch] are not necessarily in working condition, and even if they appear to work, may be unfit for a production environment.  

== How can I add a new interface language? ==

In order to add a new language (locale) to refbase, you need to perform these steps:

* Within the refbase ''locales/'' directory, copy one of the existing subdirectories and rename it to the [http://www.loc.gov/standards/iso639-2/php/code_list.php two-letter code] of the language you'd like to add (e.g. "es" in case of Spanish).
* Within your new subdirectory, translate all lines in file ''common.inc'' into your language, and save a copy of this file with encoding "Unicode (UTF-8, no BOM)" to ''common_utf8.inc''.
* Issue following MySQL command via ''sql_search.php'' when logged into refbase as admin:

 INSERT INTO languages VALUES (NULL, 'LANGCODE', 'true', '4');

In the above MySQL command, replace &lt;code&gt;LANGCODE&lt;/code&gt; with the two-letter code of your language, e.g. "es" for Spanish. In addition, you can change the last number ("4" in the above example) to alter the position at which your language name will be displayed in the language drop-down.

The new language option should now appear within the language drop-down in the refbase user options.

To see all currently available languages and to confirm that your language has been successfully added to the ''languages'' MySQL table, execute this command from within your MySQL command line interpreter (after you've selected the refbase MySQL database):

 SELECT * FROM languages;

Please note that in refbase-0.9.0, not the entire interface is available for localization. We plan to finish internationalization until version 1.0.

If you've translated the refbase interface strings in ''common.inc'' into your own language, please [[refbase:Community_Portal|send us]] this file so that we can include it with a future release of refbase.

[[Category:Configuration]]
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  <title>Troubleshooting</title>
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    <text bytes="5802" xml:space="preserve">This document lists common problems and presents possible solutions.

For problems regarding the installation process or things that don't seem to be working correctly after installation, please see [[Installation-Troubleshooting]].

For tips on how to get records from other reference managers or online services into refbase, please see [[Integration with other reference managers]] or [[Integration with online services]], respectively.

== MySQL migration and character set problems ==

To migrate your refbase installation from one computer to another, 
you need to be very careful about the character sets and MySQL versions you're using. Otherwise you will end up with garbled and strange characters when viewing what was once nice accented characters or "umlauts" (like norwegian å, æ, ø, or the german ä, ö, ü or swedish ø).

'''a)''' To solve the problem, you need to first check that the character sets used on the two database installations are the same. Use either [http://www.phpmyadmin.net/ phpMyAdmin] or the MySQL command line interpreter.

'''phpMyAdmin'''

* login and click on "Show MySQL system variables" 

* then check for these variables:

 ------------------------------------------------------------------
 Varaible:                  Session:             Global:
 ------------------------------------------------------------------
 ...
 character set client       utf8                 latin1
 character set connection   utf8                 latin1
 character set database     latin1               latin1
 character set results      utf8                 latin1
 character set server       latin1               latin1
 character set system       utf8                 utf8
 ...
 collation connection       utf8_general_ci      latin1_general_ci
 collation database         latin1_general_ci    latin1_general_ci
 collation server           latin1_general_ci    latin1_general_ci
 ...
 ------------------------------------------------------------------

'''MySQL'''

Enter the MySQL command line interpreter, select your refbase MySQL database, and execute following commands:

 mysql&gt; SHOW VARIABLES LIKE '%character%';
 mysql&gt; SHOW VARIABLES LIKE '%collation%';

Another possibility is to issue following command from the command line shell:

 mysqladmin variables | grep "character\|collation"


'''b)''' If you see discrepancies between the two database installations with respect to these variables, it is better that they coincide. This can be done by adding two lines to the "[mysqld]" section of the MySQL config file (''my.cnf'') and restarting your MySQL server. Here's an example for a latin1-based database:

 ------------------------------------------
 ...
 [mysqld]
 #init-connect = 'SET NAMES latin1'
 #init-connect = 'SET CHARACTER SET latin1'
 character-set-server = latin1
 collation-server     = latin1_general_ci
 ...
 ------------------------------------------

Note that for some MySQL systems/versions, some variable names seem to use underscores instead of hyphens. As an example, using MySQL 4.1.11 on Mac OS X 10.4, the following settings are recognized in the MySQL config file for latin1 (ISO-8859-1):

 [mysqld]
 character_set_server = latin1
 collation_server = latin1_general_ci

or, in case of UTF-8:

 [mysqld]
 character_set_server = utf8
 collation_server = utf8_general_ci


'''c)''' Next you need to "properly" dump the data from your original database, which can be achieved by use of the [http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html mysqldump] command line program. The regular mysqldump statement (without any flags) may not work correctly, because mysqldump will, by default, output data using the UTF-8 character set. So, if you're using a different character set (such as latin1), you must specify the &lt;code&gt;--default-character-set=WHAT_YOU_FIND_UNDER_character_set_server_ABOVE&lt;/code&gt; flag. And if you use an older MySQL version you may also need to use the &lt;code&gt;--compatible&lt;/code&gt; flag. Example: assuming your refbase ''latin1''-based database is named ''refbase'' and with ''root'' being the authorized user, your mysqldump statement would read:

 $ mysqldump refbase -u root -p --opt --default-character-set=latin1 &gt; refbase.sql

If you no longer have access to the old database for making this kind of dump, you may try to directly convert the old dump's character set with the iconv command line program. Here we convert the file ''dump.sql'' from UTF-8 to latin1 (ISO-8859-1) and write the data into a new file named ''iso_dump.sql'':

 $ iconv -f UTF-8 -t ISO-8859-1 dump.sql -o iso_dump.sql


'''d)''' You may want to test the new data by loading your MySQL dump file into a separate refbase database. To do so, perform these steps:

* Duplicate your refbase scripts to another directory (e.g. named "refbase_test") within your web directory.

* Copy your MySQL dump file into this new "refbase_test" directory (let's assume the dump file is named "refbase.sql").

* Within this new refbase folder, edit the ''$databaseName'' variable in file ''initialize/db.ini.php'' so that it has a name that does NOT collide with any existing MySQL database names (this is very important!).

* Access your "refbase_test" directory via the browser and point it to ''install.php''.

* On the install form, enter for "Path to the database structure file" the name of your MySQL dump file (the file from step 2, e.g. "refbase.sql").

* Edit the other fields to suit your server setup and check that the chosen default character set matches the charset of your MySQL dump file, then click the "Install" button.

The above steps can be also used to quickly setup a local read-only copy of your refbase database, e.g. on a personal laptop that is meant to be used in places without internet access.

[[Category:Troubleshooting]]</text>
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  <revision>
    <id>118</id>
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    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5820" xml:space="preserve">This document lists common problems and presents possible solutions.

For problems regarding the installation process or things that don't seem to be working correctly after installation, please see [[Installation-Troubleshooting]].

For tips on how to get records from other reference managers or online services into refbase, please see [[Integration with other reference managers]] or [[Integration with online services]], respectively.

== MySQL migration and character set problems ==

To migrate your refbase installation from one computer to another, 
you need to be very careful about the character sets and MySQL versions you're using. Otherwise you will end up with garbled and strange characters when viewing what was once nice accented characters or "umlauts" (like norwegian å, æ, ø, or the german ä, ö, ü or swedish ø).

'''a)''' To solve the problem, you need to first check that the character sets used on the two database installations are the same. Use either [http://www.phpmyadmin.net/ phpMyAdmin] or the MySQL command line interpreter.

'''phpMyAdmin'''

* login and click on "Show MySQL system variables" 

* then check for these variables:

 ------------------------------------------------------------------
 Varaible:                  Session:             Global:
 ------------------------------------------------------------------
 ...
 character set client       utf8                 latin1
 character set connection   utf8                 latin1
 character set database     latin1               latin1
 character set results      utf8                 latin1
 character set server       latin1               latin1
 character set system       utf8                 utf8
 ...
 collation connection       utf8_general_ci      latin1_general_ci
 collation database         latin1_general_ci    latin1_general_ci
 collation server           latin1_general_ci    latin1_general_ci
 ...
 ------------------------------------------------------------------

'''MySQL'''

Enter the MySQL command line interpreter, select your refbase MySQL database, and execute following commands:

 mysql&gt; SHOW VARIABLES LIKE '%character%';
 mysql&gt; SHOW VARIABLES LIKE '%collation%';

Another possibility is to issue following command from the command line shell:

 mysqladmin variables | grep "character\|collation"


'''b)''' If you see discrepancies between the two database installations with respect to these variables, it is better that they coincide. This can be done by adding two lines to the "[mysqld]" section of the MySQL config file (''my.cnf'') and restarting your MySQL server. Here's an example for a latin1-based database:

 ------------------------------------------
 ...
 [mysqld]
 #init-connect = 'SET NAMES latin1'
 #init-connect = 'SET CHARACTER SET latin1'
 character-set-server = latin1
 collation-server     = latin1_general_ci
 ...
 ------------------------------------------

Note that for some MySQL systems/versions, some variable names seem to use underscores instead of hyphens. As an example, using MySQL 4.1.11 on Mac OS X 10.4, the following settings are recognized in the MySQL config file for latin1 (ISO-8859-1):

 [mysqld]
 character_set_server = latin1
 collation_server = latin1_general_ci

or, in case of UTF-8:

 [mysqld]
 character_set_server = utf8
 collation_server = utf8_general_ci


'''c)''' Next you need to "properly" dump the data from your original database, which can be achieved by use of the [http://dev.mysql.com/doc/refman/5.0/en/mysqldump.html mysqldump] command line program. The regular mysqldump statement (without any flags) may not work correctly, because mysqldump will, by default, output data using the UTF-8 character set. So, if you're using a different character set (such as latin1), you must specify the &lt;code&gt;--default-character-set=WHAT_YOU_FIND_UNDER_character_set_server_ABOVE&lt;/code&gt; flag. And if you use an older MySQL version you may also need to use the &lt;code&gt;--compatible&lt;/code&gt; flag. Example: assuming your refbase ''latin1''-based database is named ''refbase'' and with ''root'' being the authorized user, your mysqldump statement would read:

 $ mysqldump refbase -u root -p --opt --default-character-set=latin1 &gt; refbase.sql

If you no longer have access to the old database for making this kind of dump, you may try to directly convert the old dump's character set with the iconv command line program. Here we convert the file ''dump.sql'' from UTF-8 to latin1 (ISO-8859-1) and write the data into a new file named ''iso_dump.sql'':

 $ iconv -f UTF-8 -t ISO-8859-1 dump.sql -o iso_dump.sql


'''d)''' You may want to test the new data by loading your MySQL dump file into a separate refbase database. To do so, perform these steps:

* Duplicate your refbase scripts to another directory (e.g. named "refbase_test") within your web directory.

* Copy your MySQL dump file into this new "refbase_test" directory (let's assume the dump file is named "refbase.sql").

* Within this new refbase folder, edit the ''$databaseName'' variable in file ''initialize/db.ini.php'' so that it has a name that does NOT collide with any existing MySQL database names (this is very important!).

* Access your "refbase_test" directory via the browser and point it to ''install.php''.

* On the install form, enter for "Path to the database structure file" the name of your MySQL dump file (the file from step 2, e.g. "refbase.sql").

* Edit the other fields to suit your server setup and check that the chosen default character set matches the charset of your MySQL dump file, then click the "Install" button.

The above steps can be also used to quickly setup a local read-only copy of your refbase database, e.g. on a personal laptop that is meant to be used in places without internet access.

[[Category:Troubleshooting]]
__NOEDITSECTION__</text>
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  </revision>
  <revision>
    <id>119</id>
    <parentid>118</parentid>
    <timestamp>2023-11-07T12:55:51Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="5821" xml:space="preserve">This document lists common problems and presents possible solutions.

For problems regarding the installation process or things that don't seem to be working correctly after installation, please see [[Installation-Troubleshooting]].

For tips on how to get records from other reference managers or online services into refbase, please see [[Integration with other reference managers]] or [[Integration with online services]], respectively.

== MySQL migration and character set problems ==

To migrate your refbase installation from one computer to another, 
you need to be very careful about the character sets and MySQL versions you're using. Otherwise you will end up with garbled and strange characters when viewing what was once nice accented characters or "umlauts" (like norwegian å, æ, ø, or the german ä, ö, ü or swedish ø).

'''a)''' To solve the problem, you need to first check that the character sets used on the two database installations are the same. Use either [http://www.phpmyadmin.net/ phpMyAdmin] or the MySQL command line interpreter.

'''phpMyAdmin'''

* login and click on "Show MySQL system variables" 

* then check for these variables:

 ------------------------------------------------------------------
 Varaible:                  Session:             Global:
 ------------------------------------------------------------------
 ...
 character set client       utf8                 latin1
 character set connection   utf8                 latin1
 character set database     latin1               latin1
 character set results      utf8                 latin1
 character set server       latin1               latin1
 character set system       utf8                 utf8
 ...
 collation connection       utf8_general_ci      latin1_general_ci
 collation database         latin1_general_ci    latin1_general_ci
 collation server           latin1_general_ci    latin1_general_ci
 ...
 ------------------------------------------------------------------

'''MySQL'''

Enter the MySQL command line interpreter, select your refbase MySQL database, and execute following commands:

 mysql&gt; SHOW VARIABLES LIKE '%character%';
 mysql&gt; SHOW VARIABLES LIKE '%collation%';

Another possibility is to issue following command from the command line shell:

 mysqladmin variables | grep "character\|collation"


'''b)''' If you see discrepancies between the two database installations with respect to these variables, it is better that they coincide. This can be done by adding two lines to the "[mysqld]" section of the MySQL config file (''my.cnf'') and restarting your MySQL server. Here's an example for a latin1-based database:

 ------------------------------------------
 ...
 [mysqld]
 #init-connect = 'SET NAMES latin1'
 #init-connect = 'SET CHARACTER SET latin1'
 character-set-server = latin1
 collation-server     = latin1_general_ci
 ...
 ------------------------------------------

Note that for some MySQL systems/versions, some variable names seem to use underscores instead of hyphens. As an example, using MySQL 4.1.11 on Mac OS X 10.4, the following settings are recognized in the MySQL config file for latin1 (ISO-8859-1):

 [mysqld]
 character_set_server = latin1
 collation_server = latin1_general_ci

or, in case of UTF-8:

 [mysqld]
 character_set_server = utf8
 collation_server = utf8_general_ci


'''c)''' Next you need to "properly" dump the data from your original database, which can be achieved by use of the [https://dev.mysql.com/doc/refman/8.0/en/mysqldump.html mysqldump] command line program. The regular mysqldump statement (without any flags) may not work correctly, because mysqldump will, by default, output data using the UTF-8 character set. So, if you're using a different character set (such as latin1), you must specify the &lt;code&gt;--default-character-set=WHAT_YOU_FIND_UNDER_character_set_server_ABOVE&lt;/code&gt; flag. And if you use an older MySQL version you may also need to use the &lt;code&gt;--compatible&lt;/code&gt; flag. Example: assuming your refbase ''latin1''-based database is named ''refbase'' and with ''root'' being the authorized user, your mysqldump statement would read:

 $ mysqldump refbase -u root -p --opt --default-character-set=latin1 &gt; refbase.sql

If you no longer have access to the old database for making this kind of dump, you may try to directly convert the old dump's character set with the iconv command line program. Here we convert the file ''dump.sql'' from UTF-8 to latin1 (ISO-8859-1) and write the data into a new file named ''iso_dump.sql'':

 $ iconv -f UTF-8 -t ISO-8859-1 dump.sql -o iso_dump.sql


'''d)''' You may want to test the new data by loading your MySQL dump file into a separate refbase database. To do so, perform these steps:

* Duplicate your refbase scripts to another directory (e.g. named "refbase_test") within your web directory.

* Copy your MySQL dump file into this new "refbase_test" directory (let's assume the dump file is named "refbase.sql").

* Within this new refbase folder, edit the ''$databaseName'' variable in file ''initialize/db.ini.php'' so that it has a name that does NOT collide with any existing MySQL database names (this is very important!).

* Access your "refbase_test" directory via the browser and point it to ''install.php''.

* On the install form, enter for "Path to the database structure file" the name of your MySQL dump file (the file from step 2, e.g. "refbase.sql").

* Edit the other fields to suit your server setup and check that the chosen default character set matches the charset of your MySQL dump file, then click the "Install" button.

The above steps can be also used to quickly setup a local read-only copy of your refbase database, e.g. on a personal laptop that is meant to be used in places without internet access.

[[Category:Troubleshooting]]
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<page arvcontinue="20231106215615|104">
  <title>Installation-Troubleshooting</title>
  <ns>0</ns>
  <id>30</id>
  <revision>
    <id>120</id>
    <parentid>100</parentid>
    <timestamp>2023-11-07T13:02:53Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Fix incorrect display of accented characters &amp; umlauts</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="14509" xml:space="preserve">This document presents solutions &amp; tips for installation-related problems, and for things that don't seem to be working correctly after installation.

Other issues are discussed on the generic [[Troubleshooting]] page.

If you experience any problems while installing refbase, please read this chapter before [[refbase:Community_portal|contacting us]].

== Preparations before contacting us ==

In few cases, the refbase installation shows an unwanted behaviour. This may be caused by special settings of your server setup.

'''Important''': Please check following settings and REPORT THEM when [[refbase:Community_portal|contacting us]]. This information will help us a lot to figure out what might be wrong:

* Which version of refbase do you use?
* Which platform are you using?
* Do you use a particular package such as XAMPP?
* Which versions of Apache, MySQL and PHP are you running?
* Can you execute other PHP web applications just fine? I.e., is it only refbase that is causing you trouble?
* Can you access MySQL correctly, from the command line as well as from web administration tools such as phpMyAdmin?
* Do you experience the same error/problem using a different browser or computer?
* Do you know about special config settings within your ''httpd.conf'', ''php.ini'' or ''my.cnf'' configuration files?
* Compare your ''php.ini'' with the list of [[Required_PHP-INI_Settings|required ''php.ini'' settings]] and report any differences.
* Regarding ''php.ini'' settings, especially verify that &lt;code&gt;safe_mode&lt;/code&gt; is OFF for installation. If you can't change this setting, you may need to perform a [[Manual installation|manual installation]].
* Have a look at your server's error log and report anything that may be connected with refbase.
* Please make sure that PHP error reporting is enabled and report any error messages displayed in your browser. To enable error reporting, set the following variables in your ''php.ini'' file:
 error_reporting  =  E_ALL
 display_errors = On

=== General tips ===

Please ensure that you have checked the following:

* If you're using an older refbase version, you may want to [[Updating_refbase|update]] to the newest version and see if this cures your problems.
* If you receive errors when using refbase (e.g., when adding or importing data), please try the same procedure in our [[Refbase_users|demo databases]] to check, whether this problem is specific to your own installation/data or whether it's a general issue. 
* Make sure that you've restarted your web server to apply any changes you've made to your ''php.ini'' file.
* Some installations come with multiple ''php.ini'' copies at different locations. To make sure that you're dealing with the correct ''php.ini'' file, checkout the output of the &lt;code&gt;phpinfo()&lt;/code&gt; function, it will tell you the location of the active ''php.ini'' file ([[Required_PHP-INI_Settings|more info]]). The returned status info may contain other useful information and it may help to send us the output via private mail.
* If your package manager separates php-mysql from the main php-package (eg. Fedora) make sure to install both. Otherwise every request to refbase will give an empty white page.
* Make sure that the refbase scripts have correct permission settings so that they can be accessed by your server.

== Known problems and possible solutions ==

=== Fail to login ===

If you have problems to log in with your newly created user account after installing refbase, please refer to [[Creating the first user]].

=== Upload of large files fails ===

If you're able to upload files of small file size but experience errors when attempting to upload large files, checkout the variables &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; in your active ''php.ini'' file. The values given for &lt;code&gt;post_max_size&lt;/code&gt; and &lt;code&gt;upload_max_filesize&lt;/code&gt; must be larger than the maximum file size you'd like to be able to upload (see also [[Required_PHP-INI_Settings|required ''php.ini'' settings]]).

=== Upload of files under XAMPP doesn't work ===

In some versions of [https://www.apachefriends.org/ XAMPP] the default temporary folder for uploads, as defined in ''php.ini'', is wrong:

 upload_tmp_dir = ".;c:\apachefriends\xampp\tmp"

correct would be:

 upload_tmp_dir = "c:\apachefriends\xampp\tmp"

=== Renaming of uploaded files does not work under XAMPP ===

In some versions of [https://www.apachefriends.org/ XAMPP] the needed PHP function &lt;code&gt;iconv&lt;/code&gt; is disabled. To fix this, open the ''php.ini'' file of your XAMPP distribution, search for &lt;code&gt;iconv&lt;/code&gt; and enable the function by deleting the heading comment sign (').

=== Export of records results in a blank page ===

At present, the '''ADS''', '''BibTeX''', '''EndNote''', '''ISI''', '''RIS''' and '''Word XML''' export formats require a correctly configured Bibutils while any of the other XML formats (e.g. MODS XML or ODF XML) do '''not''' depend on Bibutils. If the latter are working while the former are not, most likely the issue pertains to your [[Bibutils]] install.  

You can check that the Bibutils path was correctly configured by viewing the contents of the ''depends'' table.  The &lt;code&gt;depends_path&lt;/code&gt; for the &lt;code&gt;bibutils&lt;/code&gt; record should '''not''' be &lt;code&gt;NULL&lt;/code&gt; as seen below:  

&lt;pre&gt;
mysql&gt; SELECT * FROM depends;

+------------+------------------+-----------------+--------------+
| depends_id | depends_external | depends_enabled | depends_path |
+------------+------------------+-----------------+--------------+
|          1 | refbase          | true            | NULL         |
|          2 | bibutils         | true            | NULL         |
+------------+------------------+-----------------+--------------+
&lt;/pre&gt;

In addition, please note that:

* the path to the Bibutils programs given in table ''depends'' must end with a slash
* permissions must be set correctly so that the Bibutils programs can be executed by Apache/PHP
* if &lt;code&gt;safe_mode&lt;/code&gt; is set to On in your active ''php.ini'' file, then you'll need to put the Bibutils programs within the directory that's specified in &lt;code&gt;safe_mode_exec_dir&lt;/code&gt;
* the PHP temp/session directory must be accessible &amp; writable by Apache/PHP/Bibutils
* if you're on a hosted service, your Internet Service Provider may have given you a specific temp directory path which you may need to set explicitly in variable &lt;code&gt;$sessionTempDir&lt;/code&gt; in file ''initialize/ini.inc.php''

=== Some exports fail in refbase-0.8.0 on some win32 servers ===

Some WAMP stacks fail to execute Bibutils. A workaround is to upgrade to refbase-0.9.0 or greater.

=== Upload of files results in error message ===

If you're using refbase-0.9.0 and you're getting following error message when adding (or editing) a record that includes a file
for upload:

 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3631
 
 Warning: preg_replace() [function.preg-replace]: Unknown modifier '\' in
 .../refbase-0.9.0/includes/include.inc.php on line 3634

then you may want to upgrade to refbase-0.9.5 or greater. Alternatively, you can apply a simple patch manually:

Please open file ''modify.php'' in your refbase root directory, goto line 1100 and replace this code:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[/\\]+", true, true);

with this:

 $dirNamingScheme = trimTextPattern($dirNamingScheme, "[\/\\\\]+", true, true);

=== Import of records results in an error message ===

If you're trying to import records into your refbase database and you're getting an error message such as this one:

 There were validation errors regarding the data you entered

then you might want check whether your record format is supported by refbase and whether its syntax is correct. Please see our [[Importing records|import]] page for more information and links to example records for all supported formats.

If you're sure that your record format is supported but you still get an error message, please try to import your records at one of our [[Refbase_users|demo databases]]. If this throws up the same error message, then refbase probably has problems recognizing your record format. In that case, we'd appreciate if you'd [[refbase:Community_portal|send us]] your problematic records so that we can look into the problem.

If, however, your records import fine in our demo database, then this hints at a problem with your local refbase installation. Note that import of records in BibTeX, Copac, Endnote (tagged text or XML), PubMed XML, SciFinder or MODS XML format requires [[Bibutils]] being installed on your server. If you think that you've correctly installed Bibutils on your server and still can't get import of the above mentioned formats to work, please [[refbase:Community_portal|let us know]] and we'll try to help.

=== Undefined iconv() despite --with-iconv ===

This problem was experienced on a FreeBSD web host, and has also been reported as a [http://ca.php.net/manual/en/function.iconv.php#47428 FreeBSD issue] in the user comments at php.net, which suggests the resolution (which worked for me) to add the following block of code to the application before iconv() is called:  

&lt;pre&gt;
if (!function_exists('iconv') &amp;&amp; function_exists('libiconv')) {
   function iconv($input_encoding, $output_encoding, $string) {
       return libiconv($input_encoding, $output_encoding, $string);
   }
}
&lt;/pre&gt;

=== Problems with special characters ===

See below for some troubleshooting guidance if you have problems getting higher ASCII characters (such as accented characters or umlauts) displayed correctly in refbase, or if you cannot correctly enter or search for higher ASCII chars in the refbase web interface. Encoding problems can be really tricky since many factors interact with each other, and encoding settings can differ greatly among different systems and versions.

==== Server settings ====

First of all, you should make sure that your MySQL server's character set and collation settings are setup correctly and consistently. For more information and instructions, please see parts 'a)' and 'b)' in section [[Troubleshooting#MySQL_migration_and_character_set_problems|MySQL migration and character set problems]].

If you'd like to use refbase with UTF-8 encoding, then you'll need MySQL version 4.1.x or greater. However, in our experience, MySQL 4.1.x seems to have problems with some Unicode characters, so if possible you should use refbase in conjunction with MySQL 5.x.

It might be also worth checking your web server's configuration file (e.g., in case of the Apache web server: ''httpd.conf'' or ''apache2.conf''). On  Ubuntu, for example, some users managed to cure their encoding issues by (un)commenting (or altering) following config setting in Apache 2:

 AddDefaultCharset ISO-8859-1

==== Settings in refbase ====

When installing refbase via ''install.php'', make sure that you've chosen the desired default character set (latin1 or utf8). Be aware that if you've tried to install refbase multiple times using the same MySQL database name (in ''initialize/db.inc.php'') but with different settings as default character set, you must drop (i.e. delete) the database before installing it again with a different character encoding.

You can check the encoding of your MySQL database by issuing following command from within your MySQL command line interpreter:

 SHOW CREATE DATABASE ''DATABASE_NAME'';

In the above command, replace &lt;code&gt;''DATABASE_NAME''&lt;/code&gt; with the actual name of your refbase MySQL database.

If you've chosen "utf8" upon installation, then you have to make sure that variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; in file ''initialize/ini.inc.php'' is set to "UTF-8". And if you're using higher ASCII chars in any variable values in file ''ini.inc.php'', you should also re-save that file with encoding "Unicode (UTF-8, no BOM)".

If you've set variable &lt;code&gt;$contentTypeCharset&lt;/code&gt; to "UTF-8", you could now access refbase in your web browser and verify that the head of the HTML source states the correct encoding:

 &lt;meta http-equiv="content-type" content="text/html; charset=UTF-8"&gt;

In case of a latin1-based refbase installation, the contents of the &lt;code&gt;charset&lt;/code&gt; attribute should read "ISO-8859-1".

In order to test if refbase has been setup correctly, you should now add or edit a record via the refbase web interface and enter some special characters (such as áéíàèì or åæøöäü etc). Then, checkout again the added/edited record and verify that your entered characters display correctly. In addition, use refbase to search for these special characters and verify that your added/edited record is listed among the search results.

So, in summary, if you can 1) successfully enter special characters in refbase, 2) have them displayed correctly after saving your edits '''and''' 3) successfully search for these newly entered characters, then refbase has been set up correctly. However, if one of these actions (enter/display/search) does not work as expected, then you've still got problems.

==== Browser settings ====

If you're still experiencing problems, it's always a ''very'' good idea to try out another browser (or another browser on another platform). Also, try to manually set the encoding of your browser page to either "Unicode (UTF-8)" or "Western (ISO-8859-1)". In Firefox, this can be done via the "View &gt; Character Encoding" menu. After you've set the encoding explicitly, please see if you can now enter/display/search for higher ASCII chars successfully.

Speaking of browser settings, you can often set a default character encoding within the browser's preferences which might be also worth checking out.

==== Import and file encodings ====

Finally, note that when importing data into refbase, you have to make sure that the character encoding of your bibliographic data file matches the character encoding of your refbase database. If this is causing you any trouble, copying and pasting the data into the refbase import form may actually work better. With regard to import, you should also ensure that you're using a recent version of [[Bibutils]] since some earlier versions of Bibutils had issues with character set support.

If you still can't get rid of your encoding issues, please [[refbase:Community_portal|let us know]] and we'll see what we can do.

[[Category:Installation]]
[[Category:Troubleshooting]]
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<page arvcontinue="20231106215615|104">
  <title>Planned feature additions</title>
  <ns>0</ns>
  <id>14</id>
  <revision>
    <id>121</id>
    <parentid>33</parentid>
    <timestamp>2023-11-07T13:08:07Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Fix incorrect display of accented characters &amp; umlauts</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="24554" xml:space="preserve">This page lists planned feature additions:

'''Important''': Please note that the items listed below are simply suggestions for improving refbase and that we cannot (and don't want to) speculate on whether or when any of the listed features will be added to refbase.

== General ==

=== Resource types ===

Goal: Increase number of supported resource types.

Priority: 6

Status: added types Abstract, Conference Article, Conference Volume, Magazine Article, Manual, Miscellaneous, Newspaper Article, Report, Patent, Software

Progress: 50%

Description: refbase should allow users to choose from a variety of additional resource types including conference proceeding, patent, report, newspaper article, computer program, etc. All these types should invoke appropriate output on citation. In addition, the admin should be allowed to add additional resource types and users should be able to disable any unused types.

=== Migrate to more common libraries ===

Goal: To work under a larger number of configurations &amp; to depend on only well-maintained code.

Priority: 3

Status: not started

Progress: 0%

Description: We should consider migrating away from the ActiveLink XML library, as it isn't maintained. refbase should also be able to use MySQLi.

== Installation and updates ==

=== Redirect from ''index.php'' to ''install.php'' or ''update.php'' ===

Goal: refbase should direct to ''install.php'' or ''update.php'' as needed.

Priority: 6

Status: not started

Progress: 0%

Description: If the database doesn't exist, refbase should direct to ''install.php''. A version number or date for refbase could be stored in the database. If it is older than a version variable in ''index.php'', ''index.php'' could redirect to the update script.

=== Improvements to ''install.php'' ===

Goal: The ''install.php'' script should verify required server settings and provide more options for installation on different server setups.

Priority: 6

Status: not started

Progress: 0%

Description: 1) ''install.php'' should check required server settings prior to installation, and report possible problems in advance. 2) ''install.php'' should allow for installation into an existing database by providing an option for a table prefix that will be used for the refbase MySQL tables (currently, this can only be done by editing some configuration files). 3) To allow for web-based installation on shared hosts, ''install.php'' could offer an option to use an existing MySQL user (instead of setting up its own MySQL user which requires a MySQL admin user &amp; password). 4) ''install.php'' should provide an option to omit the sample data, i.e. install with a blank database.

=== Allow editing of configuration scripts through a web interface ===

Goal: Offer a web interface to the settings provided in ''ini.inc.php'', ''db.inc.php' and other config files.

Priority: 3

Status: not started

Progress: 0%

Description: Upon installation or update, refbase could list the settings in the various configuration files that are now manually edited &amp; allow users to make changes with the web interface.

== Searching ==

=== Search for duplicates ===

Goal: Offer the user means for handling duplicate database entries.

Priority: 4

Status: in development

Progress: 40%

Description: The database should offer means to easily spot duplicate entries and mark particular records as original (or duplicate) entry. Search features should allow users to exclude duplicate entries from the results list. It would be preferable if a smart dup detection mechanism such as phonetic matching could be used. See the [http://dev.mysql.com/doc/refman/4.1/en/string-functions.html MySQL string functions] &lt;code&gt;SOUNDEX&lt;/code&gt; and &lt;code&gt;SOUNDS LIKE&lt;/code&gt;.

=== ''OR'' search capabilities ===

Goal: Allow ''OR'' searches via the GUI.

Priority: 3

Status: not started

Progress: 0%

Description: When searching via one of the dedicated search pages, users should be able to specify whether a search on multiple fields will invoke an ''AND'' or an ''OR'' query (currently, entering search terms in multiple fields will always connect search terms with ''AND''). In addition, the "Search within Results" query form should allow users to expand the current result set, i.e. add found results to the existing list of results.

=== Simple handling of accented characters or umlauts ===

Goal: Allow naive users to search for accented characters by using the unaccented character and vice-versa.

Priority: 3

Status: not started

Progress: 0%

Description: If a search query contains no accents, it might be desirable to automatically search for commonly accented characters (especially in the Quick and Simple searches). If a user enters 'Jon', refbase could search for 'J[oóöø]n'. Similarly, it might be desirable to search for unaccented characters if a query contains an accent. If a user entered in 'Jón', refbase might search instead for 'J[oó]n'. Naturally, there should be a mechanism for "advanced users" to have exact searches (perhaps by requiring a pre or post fix for more precise handling of (un)accented search strings.

=== Cross-site searches ===

Goal: Allow users to search and display results from other databases.

Priority: 2

Status: not started

Progress: 0%

Description: refbase should allow for cross-site searches both through other installations of refbase as well as through other bibliographic databases of the [http://bibliophile.sourceforge.net/ Bibliophile initiative]. Support for web service protocols such as [[Search/Retrieve_web_services|SRU]] and [[#OpenSearch support|OpenSearch]] will ease communication between different applications.

== Adding/Editing of records ==

=== Import ===

Goal: Offer direct data import from MODS XML.

Priority: 6

Status: not started

Progress: 0%

Description: refbase currently offers a number of native import scripts, as well as scripts which use [[Bibutils]] to convert formats to something which refbase can read. Long-term plans are to provide native import capabilities for [http://www.loc.gov/standards/mods/ MODS XML]. [[Importing records]] describes the import functionality available in refbase and future plans on import.

=== Direct import via arXiv ID ===

Goal: Use arXiv API to directly fetch and import records &amp; PDFs from arXiv.org.

Priority: 5

Status: import from arXiv.org has been fully implemented, though some aspects (such as parsing of the "Journal Ref" string) might need some further testing and fine-tuning

Progress: 95%

Description: refbase allows to directly fetch and import records from [http://www.pubmed.gov PubMed.gov] via their PubMed ID. A similar feature should be added for the [http://www.arxiv.org/ arXiv.org] e-Print archive. The [http://export.arxiv.org/api_help/docs/user-manual.html arXiv API] allows for HTTP GET queries by arXiv ID and returns OpenSearch Atom feeds with basic metadata (title, author(s), publication date, abstract, and journal info if given) and any URLs (HTML, PDF, DOI) associated with an article. refbase should parse the OpenSearch response and add new database records for each feed entry. Ideally, associated PDFs would be fetched as well and stored with the record.

=== Record-type specific forms ===

Goal: Simplify manual data input by providing record-type specific forms.

Priority: 2

Status: not started

Progress: 0%

Description: Record-type specific forms would guide a user by only showing those fields that are required for a particular record-type (like journal articles, book chapters or whole books). Record-type specific forms might not be necessary if the current "Add/Edit Record" form would be able to dynamically indicate required fields for a given record-type.

=== Input validation ===

Goal: refbase should dynamically validate input in the "Add/Edit Record" form.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should provide on-the-fly validation of data while a user inputs or edits data in the "Add/Edit Record" form. This would help users to ensure correct formatting for fields that require a specific string formatting (such as the ''author'' field). Dynamic form input validation may be best realized using [http://en.wikipedia.org/wiki/AJAX AJAX] style methods.

=== Auto-filling of fields ===

Goal: refbase should auto-fill fields if possible.

Priority: 4

Status: not started

Progress: 0%

Description: refbase should be able to auto-fill empty fields based on information available in other fields and/or tables. This is especially useful if a flat database design is maintained. A typical application would be the auto-filling of journal-related fields (e.g. ''publisher'', ''place'', ''abbrev_journal'', ''language'' or ''summary_language'') from a journal database if the journal name (or ISSN) can be uniquely matched. If no journal info is available in the refbase journal database, a public service such as http://journalseek.net/ could be used for information retrieval and the fetched journal data could be automatically added to refbase's own journal database. Similarly, refbase could use web services from CrossRef (see [http://hublog.hubmed.org/archives/001624.html HubLog post] and links therein), WorldCat ([http://xissn.worldcat.org/xissnadmin/index.htm xISSN] &amp; [http://www.worldcat.org/affiliate/webservices/xisbn/app.jsp xISBN]) or LibraryThing ([http://www.librarything.com/thingology/2006/06/introducing-thingisbn_14.php thingISBN]) to supplement record metadata.

=== Auto-completion of field input ===

Goal: refbase should auto-complete user input in the "Add/Edit Record" form.

Priority: 4

Status: auto-completion has been fully implemented for the "Add/Edit Record" form and search suggestions are provided in some of the search forms (but they're not yet available in the "Advanced Search" and "Library Search" forms)

Progress: 95%

Description: It would be helpful if refbase would offer auto-completion features for fields of the "Add/Edit Record" form. This would allow users to start typing a string, then choose from a list of matching values (such as authors, keywords or journal names) that already exist in the database. Ideally, such a feature would not interfere with browser-specific auto-completion features and would be platform/browser agnostic. One way of implementing this would be a pop-up window where a generic database value browser would be combined with "Search within Results" functionality, and selected values would be written/appended to the field that's currently selected in the "Add/Edit Record" form.

=== Multiple files per record ===

Goal: refbase should allow users to upload multiple files per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to upload one file per record. It would be useful if multiple files could be attached to a given record. This would allow users to upload different representations, variants or versions of the same publication. Besides the final PDF, users could then attach a Powerpoint presentation or an audio file of an associated talk (though, in a strictly hierarchical design, talks or posters may warrant different but related records). Other use cases could be the upload of supplementary material or different manuscript revisions during collaborative preparation of an article, or the upload of a publicly available Open Access version (such as preprints or postprints). Upon upload, users should be able to specify file info (such as file type, language or a description) and access permissions individually for each file.

=== Multiple URLs per record ===

Goal: refbase should allow users to specify multiple URLs per record.

Priority: 5

Status: not started

Progress: 0%

Description: Currently, refbase allows to specify one URL per record. It would be useful if multiple URLs could be added to a given record. While the primary URL could point to the publication's entry at the publisher site, additional URLs could point to, say, further info/news about the publication, any supplementary material, or related discussion located elsewhere. As is true for multiple files, some options to categorize and/or describe the given URLs as well as individual access permissions might be useful.

=== Support foreign record identifiers ===

Goal: refbase should support record identifiers from foreign repositories (e.g. from [http://www.pubmed.gov PubMed.gov] or [http://www.arxiv.org/ arXiv.org]) explicitly, and auto-generate links back to these repositories.

Priority: 5

Status: not started

Progress: 0%

Description: Upon import, refbase currently puts foreign record identifiers (such as IDs from arXiv, ISI Web of Science, PubMed, or SciFinder) into the ''notes'' field. It would be nice, however, if these record identifiers would be stored in some dedicated field(s). This would allow refbase to auto-generate links back to the corresponding record entries at the foreign repositories.

== Sharing ==

=== Public groups (tags) ===

Goal: Allow users to collectively share and categorize groups of records.

Priority: 6

Status: not started

Progress: 0%

Description: We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system.

=== User comments ===

Goal: Allow users to comment on particular records and exchange their thoughts with others.

Priority: 3

Status: not started

Progress: 0%

Description: We imagine a comment system where multiple comments would be allowed for a particular record and where comments could be made public, group-specific or private. Comments could be searched and displayed similar to (and in combination with) bibliographic references. Here's an ASCII mockup of how we envision such a system:

 +-------------------------------------------------------------------+
 |                                                                   |
 |  Cota GF, Horne EPW (1989) Physical control of Arctic ice algal   |
 |  production. Mar Ecol Prog Ser 52(2):111-121                      |
 |                                                                   |
 |  Matthias Steffens  |  This is an essential article that provides |
 |  *****              |  a good dataset on environmental control of |
 |  2005-04-27 23:33   |  primary production in polar areas.         |
 |                                                                   |
 +-------------------------------------------------------------------+
 |                                                                   |
 |  Mock T (2002) In situ primary production in young Antarctic sea  |
 |  ice. Hydrobiologia 470(1-3):127-132                              |
 |                                                                   |
 |  Matthias Steffens  |  Given the inaccessibility of the location  |
 |  ***                |  it's valuable data nonetheless. In situ    |
 |  2004-12-18 16:05   |  measurements are still very rare.          |
 |                                                                   |
 |  Paul Miller        |  I didn't get the point of this article.    |
 |  *                  |  IMHO, it's based on a weak dataset and     |
 |  2004-12-03 12:19   |  the conclusions are fuzzy.                 |
 |                                                                   |
 |  Matthias Steffens  |  Did anybody read this one? I'd appreciate  |
 |                     |  your opinions on the used method and       |
 |  2004-12-01 11:22   |  how this relates to existing methods.      |
 |                                                                   |
 +-------------------------------------------------------------------+

According to the above visualization, comments would print below the reference they are referring to. The reference would be displayed as a citation. Multiple citations with multiple comments could be displayed and you could search within results as usual. Note the stars which indicate the users rating. Users could edit/delete their own comments and decide who'll be able to see them (everyone, certain group(s) or private).

=== Better integration with desktop reference managers ===

Goal: Provide means for easy download of records to desktop reference managers, and for direct record upload to a refbase database.

Priority: 5

Status: for [http://www.sonnysoftware.com/ Bookends], "Upload to refbase" functionality has been added

Progress: 5%

Description: refbase should integrate with desktop reference managers (such as [http://bibdesk.sourceforge.net/ BibDesk], [http://www.sonnysoftware.com/ Bookends], [http://jabref.sourceforge.net/ JabRef], [http://mekentosj.com/papers/ Papers] or [http://www.zotero.org/ Zotero]) so that records stored in a refbase database can be easily retrieved from within these applications. Zotero can already extract bibliographic metadata from refbase's web pages via [[COinS]] or [[unAPI service|unAPI]], and something similar could work for other apps that feature web views. In addition, it would be desirable if users could search an online refbase database from within their desktop reference managers. The refbase search &amp; retrieve webservices offer standardized APIs for this, such as the [[Search/Retrieve_web_services|SRU/W webservice]] or [[#OpenSearch support|OpenSearch]] in conjunction with the existing [[unAPI service]]. Finally, it would be also useful if users of desktop reference managers could upload (and eventually synch) records to a refbase server directly from within their desktop application. In case of Zotero, "upload to refbase" functionality could be developed via an [http://dev.zotero.org/docs/sample_utility Zotero utility].

== Webservices ==

=== OpenSearch support ===

Goal: Allow OpenSearch clients to query refbase and return found results in OpenSearch response format.

Priority: 6

Status: OpenSearch support has been implemented with support for auto-discovery, multiple response formats (HTML, Atom, RSS, SRW_DC XML, SRW_MODS XML), simple CQL searches and support for search suggestions (returned in JSON or HTML); a better CQL parser would be desirable

Progress: 95%

Description: Similar to the refbase [[Search/Retrieve_web_services|SRU/W webservice]], refbase should support an [[OpenSearch service|OpenSearch]] webservice. OpenSearch capable clients would be able to [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_Query_element query] a refbase database and retrieve search results in an OpenSearch [http://www.opensearch.org/Specifications/OpenSearch/1.1#OpenSearch_response_elements response format], e.g. RSS 2.0 or Atom 1.0, plus the OpenSearch response extensions. This would also allow to integrate several refbase servers (or other OpenSearch capable servers) via [[Planned_feature_additions#Cross-site_searches|cross-site searches]]. When implemented, refbase should support auto-discovery to allow for [http://developer.mozilla.org/en/docs/Creating_OpenSearch_plugins_for_Firefox search plugins]. Eventual support for JSON for fetching of search suggestions would be nice.

=== API ===

Goal: Provide an API that allows clients to query a refbase database, retrieve results in a structured format and modify any database information.

Priority: 5

Status: not started

Progress: 0%

Description: Opposed to pure search/retrieve webservices (such as [[Search/Retrieve_web_services|SRU/W]] and [[OpenSearch service|OpenSearch]]), a [http://en.wikipedia.org/wiki/Representational_State_Transfer RESTful] API should also allow clients to send requests that ''alter'' the database, i.e. add, edit or delete records, meta-data or users. This will allow for easy integration with third-party tools and enable the development of alternative interfaces to a refbase database. It would be desirable to support an existing framework such as Google's [http://code.google.com/apis/gdata/index.html GData], [http://www.ukoln.ac.uk/repositories/digirep/index/SWORD SWORD] (Simple Web-service Offering Repository Deposit), or the [http://www.loc.gov/standards/sru/record-update/ Record Update service] that is proposed by the SRU community.

=== OAI Protocol for Metadata Harvesting ===

Goal: Provide (yet another) standard way for software to retrieve information from refbase. Eventually provide a mechanism for retrieval from arxiv/dspace/eprints, and other software which is targeted at larger institutions.

Priority: 5

Status: implemented support for the simple/unqualified Dublin Core (OAI_DC) XML format which is a prerequisite for OAI-PMH

Progress: 10%

Description: [http://www.openarchives.org/OAI/openarchivesprotocol.html The Open Archives Initiative Protocol for Metadata Harvesting], which is implemented by [http://software.eprints.org/ EPrints] and [http://www.dspace.org/ DSpace] uses Dublin Core XML over HTTP. This is harvested by google and yahoo and others.

== Citation support ==

=== Increase number of available citation styles ===

Goal: Add most commonly used citation styles and generally increase the number of available styles.

Priority: 6

Status: added styles: AMA, APA, Chicago, Harvard (3 variants), MLA, Vancouver

Progress: 75%

Description: By default, refbase should include at least the most universal styles (i.e. APA, MLA, Chicago, Harvard, Turabian, CB, CGOS, CBE, AMA). Besides that, it would be nice to increase the list of available citation styles substantially.

=== User-customizable citation styles ===

Goal: Allow users to create custom citation styles, preferably via the use of a plugin structure.

Priority: 4

Status: not started

Progress: 0%

Description: Currently, citation styles are defined as PHP functions which is very powerful but not very user friendly. We plan to enhance the cite feature by adding support for other (more general) citation formats. We'd like to integrate refbase with other solutions which offer users an easier way of adding or editing any citation styles. Projects such as Mark Grimshaw's [http://sourceforge.net/project/showfiles.php?group_id=113285&amp;package_id=150961 OSBib] or [http://xbiblio.sourceforge.net/ xbiblio] developed by Bruce D'Arcus come to mind. Some implementation of CSL (backed by Bruce and used by Zotero) would be nice.

== Export ==

== Access permissions ==

=== Record-specific permissions ===

Goal: Offer fine-grained access control on record-level.

Priority: 6

Status: not started

Progress: 0%

Description: The creator (or the admin) of a record should be able to specify who will be allowed to view a particular record. For each record, an authorized user should be able to set the record visibility to everyone, private or to particular groups of database users. Separate access control settings should be provided for file downloads and edits.

== Metadata and Microformats ==

=== Embedded RDF ===

Goal: Embed citation metadata in HTML pages as machine-readable RDF which may be processed by clients.

Priority: 5

Status: not started

Progress: 0%

Description: [http://en.wikipedia.org/wiki/Resource_Description_Framework RDF] is less supported than [[COinS]], but is a useful alternative that has some advantages (such as multiple author support). This will allow client-side tools (such as [http://www.zotero.org/ Zotero]) to more easily use the data provided by refbase.

=== Other microformats? ===

Goal: Other formats may be useful as well

Priority: 1

Status: not started

Progress: 0%

Description: [http://microformats.org/wiki/citation Other citation microformats] and a [http://microformats.org/wiki/search-results-example search results microformat] might eventually be useful. It seems like COinS is the most useful at this point in time, though.

=== Wikipedia citations &amp; other UnAPI goodness ===

Goal: Make it easy for WP contributors to use refbase deployments to add articles

Priority:

Status: not started

Progress: 0%

Description: WP's citation templates are pretty straightforward clips of text, a'la:
 &lt;nowiki&gt;{{cite journal | author = Greiner C, Oppenheimer SM, Dunand DC | title = High strength, low stiffness, porous NiTi with superelastic properties. | journal = Acta Biomater | volume = 1 | issue = 6 | pages = 705-16 | year = 2005 | id = PMID 16701851}}&lt;/nowiki&gt;
[http://www.hubmed.org/ Hubmed] has a good example of UnAPIed Wikipedia citation generation.  They also have del.icio.us bookmarking (I guess we could add less obtrusive citeulike/connotea/etc. links this way).


[[Category:General]]
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<page arvcontinue="20231106215615|104">
  <title>Interface</title>
  <ns>0</ns>
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  <revision>
    <id>122</id>
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    </contributor>
    <comment>Original page content from 07-Feb-2006</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="678" xml:space="preserve">Use the links below to learn more about the refbase interface:

* [[Main page]]:
** [[Show My Refs]]
** [[Quick Search]]
** [[Browse My Refs]]
** [[Show My Group]]
** [[Recall My Query]]

* Search pages:
** [[Simple Search]]
** [[Advanced Search]]
** [[SQL Search]]
** [[Library Search]]

* Views:
** [[List View]]
** [[Details View]]
** [[Print View]]
** [[Browse View]]
** [[Citation View]]
** [[Export View]]

* Forms on results pages:
** [[Show My Group]]
** [[Search within Results]]
** [[Display Options]]
** [[Display full Entries]]
** [[Cite]]
** [[Add or Remove Group]]
** [[Export]]

* Special Pages:
** [[Display Details]]
** [[Extract Citations]]

[[Category:Usage]]</text>
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<page arvcontinue="20231106215615|104">
  <title>Recall My Query</title>
  <ns>0</ns>
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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 05-Jan-2007</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3181" xml:space="preserve">refbase offers to save any of your queries for easy later retrieval. In addition, refbase will store the following display options with your query:

* name (and order) of displayed fields
* number of records displayed per page
* sort order of records
* if links and/or SQL query are displayed
* view type (i.e., web view or print view)

This means that you can use the 'save query' functionality to save custom views.

== Example 1 ==

Say, you regularly find yourself scanning the abstracts within your own literature. To save a custom view for that purpose, perform the following steps:

* Login and click on the 'My Refs' link in the upper right corner. This will show all records belonging to your own literature data set.
* Adopt the column view to fit your needs, i.e., use the 'Display Options' form to hide, say, the ''publication'', ''volume'' and ''pages'' fields and show the ''abstract'' field instead. You may also want to increase the number of records being displayed per page.
* Now click the 'save' link in the header line that says "x-x of xxx records found matching your query (save | RSS)".
* You'll see a form containing your current query. If you want, you can further refine your query or any display options here (like suppressing the 'Links' column or choosing 'Print' view for display). If you're done, give your query a meaningful name and click the 'Add Query' button.

You can now always access your saved query from the drop down of the 'Recall My Query' form on the main page. Note that the items in the drop down are sorted by history of usage, i.e., most recently chosen queries will be always at the top of the list.

The forms in the header of your search results list (i.e., 'Show My Group', 'Search within Results' and 'Display Options') will respect your current view settings. By this, you can perform a search within your own literature or display a different group but still have, say, the ''abstract'' field displayed instead of the default set of columns.

== Example 2 ==

Another use of the 'save query' feature might be the quick access to hidden fields (or fields not shown in the drop down menus) that you would otherwise need to type in manually using the SQL search form.

As an example, refbase offers hidden fields that store information about when a record was created/modified and who did create/modify the record. To save a custom query/view that displays modification info for all records that were edited today, perform the following steps:

* Click the 'save' link in the header line of any search results page or call the ''query_manager.php'' script directly using the URL field of your browser.
* Select the displayed SQL query and replace it with this one:
 SELECT author, title, year, location, modified_by, modified_date, modified_time FROM refs WHERE modified_date = CURDATE() ORDER BY modified_date DESC, modified_time DESC
* Adopt the display options as desired, name your query (e.g., 'Edited Today') and click the 'Add Query' button.

Selecting this query (from the drop down of the 'Recall My Query' form on the main page) will give you an instant overview of who edited what during the day.

[[Category:Usage]]</text>
    <sha1>49a8de677a3042b35571002a85249106bef535d3</sha1>
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  <revision>
    <id>124</id>
    <parentid>123</parentid>
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      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="3199" xml:space="preserve">refbase offers to save any of your queries for easy later retrieval. In addition, refbase will store the following display options with your query:

* name (and order) of displayed fields
* number of records displayed per page
* sort order of records
* if links and/or SQL query are displayed
* view type (i.e., web view or print view)

This means that you can use the 'save query' functionality to save custom views.

== Example 1 ==

Say, you regularly find yourself scanning the abstracts within your own literature. To save a custom view for that purpose, perform the following steps:

* Login and click on the 'My Refs' link in the upper right corner. This will show all records belonging to your own literature data set.
* Adopt the column view to fit your needs, i.e., use the 'Display Options' form to hide, say, the ''publication'', ''volume'' and ''pages'' fields and show the ''abstract'' field instead. You may also want to increase the number of records being displayed per page.
* Now click the 'save' link in the header line that says "x-x of xxx records found matching your query (save | RSS)".
* You'll see a form containing your current query. If you want, you can further refine your query or any display options here (like suppressing the 'Links' column or choosing 'Print' view for display). If you're done, give your query a meaningful name and click the 'Add Query' button.

You can now always access your saved query from the drop down of the 'Recall My Query' form on the main page. Note that the items in the drop down are sorted by history of usage, i.e., most recently chosen queries will be always at the top of the list.

The forms in the header of your search results list (i.e., 'Show My Group', 'Search within Results' and 'Display Options') will respect your current view settings. By this, you can perform a search within your own literature or display a different group but still have, say, the ''abstract'' field displayed instead of the default set of columns.

== Example 2 ==

Another use of the 'save query' feature might be the quick access to hidden fields (or fields not shown in the drop down menus) that you would otherwise need to type in manually using the SQL search form.

As an example, refbase offers hidden fields that store information about when a record was created/modified and who did create/modify the record. To save a custom query/view that displays modification info for all records that were edited today, perform the following steps:

* Click the 'save' link in the header line of any search results page or call the ''query_manager.php'' script directly using the URL field of your browser.
* Select the displayed SQL query and replace it with this one:
 SELECT author, title, year, location, modified_by, modified_date, modified_time FROM refs WHERE modified_date = CURDATE() ORDER BY modified_date DESC, modified_time DESC
* Adopt the display options as desired, name your query (e.g., 'Edited Today') and click the 'Add Query' button.

Selecting this query (from the drop down of the 'Recall My Query' form on the main page) will give you an instant overview of who edited what during the day.

[[Category:Usage]]
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  <title>Library Search</title>
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    </contributor>
    <comment>Rough version of the original page content (recovered from https://web.archive.org/web/20160427032455/http://www.refbase.net/index.php/Library_Search)</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4048" xml:space="preserve">The "library search," is a special one-click search, offered directly at the start page and in the footer of every page. The refbase admin can configure which subset of the database the "library search" uses.

== Changing the library search ==

This chapter is solely relavant for the refbase admin

=== Definition of what this search is searching for ===

The 'library_search.php' script will search within a subset of your refbase database. Searches via this library search form will be restricted to the condition given in variable '$librarySearchPattern' in file 'initialize/ini.inc.php'.

There you will find this explanation:

&gt; Define what will be searched by "library_search.php": refbase offers a "Library Search" feature that provides a separate search page for searching an institution's library. All searches performed thru this search form will be restricted to records that match the specified condition. First param must be a valid field name from table 'refs', second param the conditional expression (specified as MySQL extended regular expression -&gt; see note at the end of this file). Of course, you could also use this feature to restrict searches thru "library_search.php" by _any_ other condition. E.g., with "location" as the first parameter and your own login email address as the second parameter, any "library" search would be restricted to your personal literature data set.

If, for example, items of your institute's library are also catalogued in your refbase database, then you could use the library search feature to only search items in your institute's library.

At the Institute for Polarecology Kiel, we add items of our local library to our refbase database using a dedicated refbase account (named "Library Admin" or the like). We've then set variable '$librarySearchPattern' in 'ini.inc.php' to:

 $librarySearchPattern = array("location", "library"); // e.g. 'array("location", "IPÖ Library")'

This will restrict searches via 'library_search.php' to records that contain the word "Library" within the 'location' field. Thus search results will only show items from our institute's library. The search results list will also display additional/different fields by default, such as the 'call_number' field (which contains the unique library identifier for the item).

You could, instead, search results to items that contain a particular author, publication, keyword, contribution_id, etc. As an example, consider that you've tagged a particular subset of your database records with the word "Students Reading List" in the 'keywords' field. Then you could use this setup:

	$librarySearchPattern = array("keywords", "Students Reading List");

to restrict searches via 'library_search.php' to records that contain the keyword "Students Reading List".

=== Changing the name of "library search" ===

Since the name of the standard-link 'library search' is sometimes confusing (especially, if you define your own query), you can change this in one of two ways. Both involve modifying refbase files which will be overwritten on upgrades.

==== Customized localization ====

"Library" and "Search" are defined in the language-file 'locales/common.inc'. You can modify "Library" to make it more descriptive.


==== Alternative: customize index.php ====

1. Open 'index.php' of your refbase installation.
Search for this line:

	&lt;li&gt;&lt;a href="library_search.php"&gt;&lt;?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?&gt;

and replace this

	?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?

part of the line with your desired link name.

2. Open the 'includes/footer.inc.php' file and search for 'library'

you have to change the 'title'-parameter and the link name.


For these changes, you may either use static names (which will remove the localization of refbase for your users) or define new localized variables.


== Hiding the link ==

An alternative to customizing the search is to remove it completely. One can safely comment out or remove the lines in 'index.php' and 'includes/footer.inc.php'.</text>
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    <comment>Better wikitext approximation of the original page content</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="4346" xml:space="preserve">The "library search" is a special one-click search, offered directly at the start page and in the footer of every page. The refbase admin can configure which subset of the database the "library search" uses.

== Changing the library search ==

This chapter is solely relavant for the refbase admin

=== Definition of what this search is searching for ===

The &lt;code&gt;library_search.php&lt;/code&gt; script will search within a subset of your refbase database. Searches via this library search form will be restricted to the condition given in variable &lt;code&gt;$librarySearchPattern&lt;/code&gt; in file &lt;code&gt;initialize/ini.inc.php&lt;/code&gt;.

There you will find this explanation:

&lt;blockquote&gt;
Define what will be searched by &lt;code&gt;library_search.php&lt;/code&gt;: refbase offers a "Library Search" feature that provides a separate search page for searching an institution's library. All searches performed thru this search form will be restricted to records that match the specified condition. First param must be a valid field name from table &lt;code&gt;refs&lt;/code&gt;, second param the conditional expression (specified as MySQL extended regular expression -&gt; see note at the end of this file). Of course, you could also use this feature to restrict searches thru &lt;code&gt;library_search.php&lt;/code&gt; by _any_ other condition. E.g., with &lt;code&gt;location&lt;/code&gt; as the first parameter and your own login email address as the second parameter, any "library" search would be restricted to your personal literature data set.
&lt;/blockquote&gt;

If, for example, items of your institute's library are also catalogued in your refbase database, then you could use the library search feature to only search items in your institute's library.

At the Institute for Polarecology Kiel, we add items of our local library to our refbase database using a dedicated refbase account (named "Library Admin" or the like). We've then set variable &lt;code&gt;$librarySearchPattern&lt;/code&gt; in &lt;code&gt;ini.inc.php&lt;/code&gt; to:

 $librarySearchPattern = array("location", "library"); // e.g. &lt;code&gt;array("location", "IPÖ Library")&lt;/code&gt;

This will restrict searches via &lt;code&gt;library_search.php&lt;/code&gt; to records that contain the word "Library" within the &lt;code&gt;location&lt;/code&gt; field. Thus search results will only show items from our institute's library. The search results list will also display additional/different fields by default, such as the &lt;code&gt;call_number&lt;/code&gt; field (which contains the unique library identifier for the item).

You could, instead, search results to items that contain a particular author, publication, keyword, contribution_id, etc. As an example, consider that you've tagged a particular subset of your database records with the word "Students Reading List" in the &lt;code&gt;keywords&lt;/code&gt; field. Then you could use this setup:

 $librarySearchPattern = array("keywords", "Students Reading List");

to restrict searches via &lt;code&gt;library_search.php&lt;/code&gt; to records that contain the keyword "Students Reading List".

=== Changing the name of "library search" ===

Since the name of the standard-link &lt;code&gt;library search&lt;/code&gt; is sometimes confusing (especially, if you define your own query), you can change this in one of two ways. Both involve modifying refbase files which will be overwritten on upgrades.

==== Customized localization ====

"Library" and "Search" are defined in the language-file &lt;code&gt;locales/common.inc&lt;/code&gt;. You can modify "Library" to make it more descriptive.

==== Alternative: customize index.php ====

* Open &lt;code&gt;index.php&lt;/code&gt; of your refbase installation.

Search for this line:

&lt;pre&gt;
&lt;li&gt;&lt;a href="library_search.php"&gt;&lt;?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?&gt;
&lt;/pre&gt;

and replace this

&lt;pre&gt;
?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?
&lt;/pre&gt;

part of the line with your desired link name.

* Open the &lt;code&gt;includes/footer.inc.php&lt;/code&gt; file and search for &lt;code&gt;library&lt;/code&gt;

you have to change the &lt;code&gt;title&lt;/code&gt;-parameter and the link name.

For these changes, you may either use static names (which will remove the localization of refbase for your users) or define new localized variables.


== Hiding the link ==

An alternative to customizing the search is to remove it completely. One can safely comment out or remove the lines in &lt;code&gt;index.php&lt;/code&gt; and &lt;code&gt;includes/footer.inc.php&lt;/code&gt;.</text>
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    <text bytes="4365" xml:space="preserve">The "library search" is a special one-click search, offered directly at the start page and in the footer of every page. The refbase admin can configure which subset of the database the "library search" uses.

== Changing the library search ==

This chapter is solely relavant for the refbase admin

=== Definition of what this search is searching for ===

The &lt;code&gt;library_search.php&lt;/code&gt; script will search within a subset of your refbase database. Searches via this library search form will be restricted to the condition given in variable &lt;code&gt;$librarySearchPattern&lt;/code&gt; in file &lt;code&gt;initialize/ini.inc.php&lt;/code&gt;.

There you will find this explanation:

&lt;blockquote&gt;
Define what will be searched by &lt;code&gt;library_search.php&lt;/code&gt;: refbase offers a "Library Search" feature that provides a separate search page for searching an institution's library. All searches performed thru this search form will be restricted to records that match the specified condition. First param must be a valid field name from table &lt;code&gt;refs&lt;/code&gt;, second param the conditional expression (specified as MySQL extended regular expression -&gt; see note at the end of this file). Of course, you could also use this feature to restrict searches thru &lt;code&gt;library_search.php&lt;/code&gt; by _any_ other condition. E.g., with &lt;code&gt;location&lt;/code&gt; as the first parameter and your own login email address as the second parameter, any "library" search would be restricted to your personal literature data set.
&lt;/blockquote&gt;

If, for example, items of your institute's library are also catalogued in your refbase database, then you could use the library search feature to only search items in your institute's library.

At the Institute for Polarecology Kiel, we add items of our local library to our refbase database using a dedicated refbase account (named "Library Admin" or the like). We've then set variable &lt;code&gt;$librarySearchPattern&lt;/code&gt; in &lt;code&gt;ini.inc.php&lt;/code&gt; to:

 $librarySearchPattern = array("location", "library"); // e.g. &lt;code&gt;array("location", "IPÖ Library")&lt;/code&gt;

This will restrict searches via &lt;code&gt;library_search.php&lt;/code&gt; to records that contain the word "Library" within the &lt;code&gt;location&lt;/code&gt; field. Thus search results will only show items from our institute's library. The search results list will also display additional/different fields by default, such as the &lt;code&gt;call_number&lt;/code&gt; field (which contains the unique library identifier for the item).

You could, instead, search results to items that contain a particular author, publication, keyword, contribution_id, etc. As an example, consider that you've tagged a particular subset of your database records with the word "Students Reading List" in the &lt;code&gt;keywords&lt;/code&gt; field. Then you could use this setup:

 $librarySearchPattern = array("keywords", "Students Reading List");

to restrict searches via &lt;code&gt;library_search.php&lt;/code&gt; to records that contain the keyword "Students Reading List".

=== Changing the name of "library search" ===

Since the name of the standard-link &lt;code&gt;library search&lt;/code&gt; is sometimes confusing (especially, if you define your own query), you can change this in one of two ways. Both involve modifying refbase files which will be overwritten on upgrades.

==== Customized localization ====

"Library" and "Search" are defined in the language-file &lt;code&gt;locales/common.inc&lt;/code&gt;. You can modify "Library" to make it more descriptive.

==== Alternative: customize index.php ====

* Open &lt;code&gt;index.php&lt;/code&gt; of your refbase installation.

Search for this line:

&lt;pre&gt;
&lt;li&gt;&lt;a href="library_search.php"&gt;&lt;?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?&gt;
&lt;/pre&gt;

and replace this

&lt;pre&gt;
?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?
&lt;/pre&gt;

part of the line with your desired link name.

* Open the &lt;code&gt;includes/footer.inc.php&lt;/code&gt; file and search for &lt;code&gt;library&lt;/code&gt;

you have to change the &lt;code&gt;title&lt;/code&gt;-parameter and the link name.

For these changes, you may either use static names (which will remove the localization of refbase for your users) or define new localized variables.


== Hiding the link ==

An alternative to customizing the search is to remove it completely. One can safely comment out or remove the lines in &lt;code&gt;index.php&lt;/code&gt; and &lt;code&gt;includes/footer.inc.php&lt;/code&gt;.

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    <text bytes="4364" xml:space="preserve">The "library search" is a special one-click search, offered directly at the start page and in the footer of every page. The refbase admin can configure which subset of the database the "library search" uses.

== Changing the library search ==

This chapter is solely relavant for the refbase admin

=== Definition of what this search is searching for ===

The &lt;code&gt;library_search.php&lt;/code&gt; script will search within a subset of your refbase database. Searches via this library search form will be restricted to the condition given in variable &lt;code&gt;$librarySearchPattern&lt;/code&gt; in file &lt;code&gt;initialize/ini.inc.php&lt;/code&gt;.

There you will find this explanation:

&lt;blockquote&gt;
Define what will be searched by &lt;code&gt;library_search.php&lt;/code&gt;: refbase offers a "Library Search" feature that provides a separate search page for searching an institution's library. All searches performed thru this search form will be restricted to records that match the specified condition. First param must be a valid field name from table &lt;code&gt;refs&lt;/code&gt;, second param the conditional expression (specified as MySQL extended regular expression -&gt; see note at the end of this file). Of course, you could also use this feature to restrict searches thru &lt;code&gt;library_search.php&lt;/code&gt; by _any_ other condition. E.g., with &lt;code&gt;location&lt;/code&gt; as the first parameter and your own login email address as the second parameter, any "library" search would be restricted to your personal literature data set.
&lt;/blockquote&gt;

If, for example, items of your institute's library are also catalogued in your refbase database, then you could use the library search feature to only search items in your institute's library.

At the Institute for Polarecology Kiel, we add items of our local library to our refbase database using a dedicated refbase account (named "Library Admin" or the like). We've then set variable &lt;code&gt;$librarySearchPattern&lt;/code&gt; in &lt;code&gt;ini.inc.php&lt;/code&gt; to:

 $librarySearchPattern = array("location", "library"); // e.g. &lt;code&gt;array("location", "IPÖ Library")&lt;/code&gt;

This will restrict searches via &lt;code&gt;library_search.php&lt;/code&gt; to records that contain the word "Library" within the &lt;code&gt;location&lt;/code&gt; field. Thus search results will only show items from our institute's library. The search results list will also display additional/different fields by default, such as the &lt;code&gt;call_number&lt;/code&gt; field (which contains the unique library identifier for the item).

You could, instead, search results to items that contain a particular author, publication, keyword, contribution_id, etc. As an example, consider that you've tagged a particular subset of your database records with the word "Students Reading List" in the &lt;code&gt;keywords&lt;/code&gt; field. Then you could use this setup:

 $librarySearchPattern = array("keywords", "Students Reading List");

to restrict searches via &lt;code&gt;library_search.php&lt;/code&gt; to records that contain the keyword "Students Reading List".

=== Changing the name of "library search" ===

Since the name of the standard-link &lt;code&gt;library search&lt;/code&gt; is sometimes confusing (especially, if you define your own query), you can change this in one of two ways. Both involve modifying refbase files which will be overwritten on upgrades.

==== Customized localization ====

"Library" and "Search" are defined in the language-file &lt;code&gt;locales/common.inc&lt;/code&gt;. You can modify "Library" to make it more descriptive.

==== Alternative: customize index.php ====

* Open &lt;code&gt;index.php&lt;/code&gt; of your refbase installation.

Search for this line:

&lt;pre&gt;
&lt;li&gt;&lt;a href="library_search.php"&gt;&lt;?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?&gt;
&lt;/pre&gt;

and replace this

&lt;pre&gt;
?php echo $loc["Library"]; ?&gt; &lt;?php echo $loc["Search"]; ?
&lt;/pre&gt;

part of the line with your desired link name.

* Open the &lt;code&gt;includes/footer.inc.php&lt;/code&gt; file and search for &lt;code&gt;library&lt;/code&gt;

you have to change the &lt;code&gt;title&lt;/code&gt;-parameter and the link name.

For these changes, you may either use static names (which will remove the localization of refbase for your users) or define new localized variables.

== Hiding the link ==

An alternative to customizing the search is to remove it completely. One can safely comment out or remove the lines in &lt;code&gt;index.php&lt;/code&gt; and &lt;code&gt;includes/footer.inc.php&lt;/code&gt;.

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<page arvcontinue="20231106215615|104">
  <title>Interface FAQ</title>
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    <model>wikitext</model>
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    <text bytes="1799" xml:space="preserve">This page lists some frequently asked questions about the refbase interface:

== Where can I change the citation style? ==

You can change the citation style in the "Display Options" form when you're in Citation view. Here's how to do it:

# Perform your search as usual. 
# Above the list of your search results, click on the "Citations" link (it's on the right-hand side of the screen). This will display your search results in Citation view.
# Now click the "Search &amp; Display Options" link (it's also above the list of search results, on the left-hand side of the screen). This will display some forms that let you refine your query or change the display of results.
# Choose your preferred citation style from the "Style" dropdown menu in the "Display Options" form, then click the "Show" button that's next to the dropdown menu.

Your chosen citation style should now get used for all citation output on the web interface as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. See also the next FAQ entry.

== Can I specify my own default citation style? ==

While the database admin can choose a global default style ([[Configuring_refbase#How_can_I_change_the_default_citation_style.3F|more info]]), there currently isn't an option to choose the default citation style individually for each user. However, as long as you stay in the search results list, your selected citation style will be honoured &amp;mdash; even when switching between views, using any of the search &amp; display options, or when performing new searches via the Quick Search form (at the top right corner of the screen).

== How can I delete records? ==

The [[Deleting records]] pages describes how to remove record entries from the database, and explains how to achieve batch deletions.

[[Category:Usage]]</text>
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    <text bytes="1817" xml:space="preserve">This page lists some frequently asked questions about the refbase interface:

== Where can I change the citation style? ==

You can change the citation style in the "Display Options" form when you're in Citation view. Here's how to do it:

# Perform your search as usual. 
# Above the list of your search results, click on the "Citations" link (it's on the right-hand side of the screen). This will display your search results in Citation view.
# Now click the "Search &amp; Display Options" link (it's also above the list of search results, on the left-hand side of the screen). This will display some forms that let you refine your query or change the display of results.
# Choose your preferred citation style from the "Style" dropdown menu in the "Display Options" form, then click the "Show" button that's next to the dropdown menu.

Your chosen citation style should now get used for all citation output on the web interface as well as for export of formatted citation lists to RTF, PDF, LaTeX, etc. See also the next FAQ entry.

== Can I specify my own default citation style? ==

While the database admin can choose a global default style ([[Configuring_refbase#How_can_I_change_the_default_citation_style.3F|more info]]), there currently isn't an option to choose the default citation style individually for each user. However, as long as you stay in the search results list, your selected citation style will be honoured &amp;mdash; even when switching between views, using any of the search &amp; display options, or when performing new searches via the Quick Search form (at the top right corner of the screen).

== How can I delete records? ==

The [[Deleting records]] pages describes how to remove record entries from the database, and explains how to achieve batch deletions.

[[Category:Usage]]
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<page arvcontinue="20231106215615|104">
  <title>Searching</title>
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    <model>wikitext</model>
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    <text bytes="9903" xml:space="preserve">This page explains how to use the refbase search facilities:

== Search options ==

=== Basic search ===

* [[Quick Search]]

=== Search pages ===

* [[Simple Search]]
* [[Advanced Search]]
* [[SQL Search]]
* [[Library Search]]

=== Refine your search results ===

* [[Search within Results]]
* [[SQL Search]]

=== Directly jump to particular records ===

* [[Display Details]]

=== User-specific search options ===

* [[Show My Refs]]
* [[Show My Group]]
* [[Recall My Query]]
* [[Display Details]]

== Search syntax ==

=== Basic queries ===

When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string. As an example, searching the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=arctic arctic]

will return records where the ''title'' field contains "Arctic", "Antarctic", "Antarctica", "Antarcticque" "subarctic", etc.

This "contains" search is the standard search behaviour in simple search forms such as the [[Quick Search]] or [[Search within Results]] forms. It is also used in all other search forms if "contains" or "does not contain" is selected in the drop-down that specifies the search mode.

If your search string consists of several words, refbase will return all records where the searched field literally contains the given string of words. E.g., if you searched in the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=sea%20ice%20thickness sea ice thickness]

then refbase will return any records whose title exactly contains the string "sea ice thickness". This means that you don't need to enclose a string with quotation marks to force an exact match (as is the case for various online search engines such as Google). When searching a refbase database, quotation marks are treated as regular characters and have no special meaning.

Now, what if you wanted to search a database field for the occurrence of two words which are not necessarily next to each other? In refbase, the easiest way of searching for something like "contains &lt;code&gt;xxx&lt;/code&gt; AND contains &lt;code&gt;yyy&lt;/code&gt;" is to simply start your search with the first search term (&lt;code&gt;xxx&lt;/code&gt;), then use the [[Search within Results]] form above the search results list to search for the second search term (&lt;code&gt;yyy&lt;/code&gt;). Using this method, you can quickly perform complex searches on multiple fields (and using multiple search terms) without the need of figuring out the correct search pattern in advance.

When searching for two (or more) authors of a particular paper, you often know the order in which the two authors occur. In this case you can make use of the &lt;code&gt;.+&lt;/code&gt; metacharacter sequence which matches any string of characters (more on metacharacters below). As an example, you can use:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=Cota%2E%2BSmith&amp;without=dups Cota.+Smith]

to find all records where the ''author'' field contains "Cota" followed by "Smith".

=== Using metacharacters to form complex queries ===

By default, refbase allows you to use metacharacters to describe a more complex search pattern. The deployed search syntax is called [http://en.wikipedia.org/wiki/Regular_expressions regular expressions] (often abbreviated as regexp or regex) which comes in many flavors. refbase supports MySQL regular expressions via use of the MySQL &lt;code&gt;REGEXP&lt;/code&gt; (or &lt;code&gt;RLIKE&lt;/code&gt;) syntax. The MySQL website offers an introduction on [http://dev.mysql.com/doc/refman/5.0/en/pattern-matching.html pattern matching] and provides more information about the [http://dev.mysql.com/doc/refman/5.0/en/regexp.html &lt;code&gt;REGEXP&lt;/code&gt; syntax] for regular expressions. See the examples section below for some simple usage examples.

While regular expressions provide a powerful syntax for searching they may be somewhat difficult to write and daunting if you're new to the concept of regular expressions. There are various [http://directory.google.com/Top/Computers/Programming/Languages/Regular_Expressions/FAQs,_Help,_and_Tutorials/ tutorials on regular expressions] on the net that can help you getting started. A nice [http://etext.lib.virginia.edu/helpsheets/regex.html basic introduction to regular expressions] was written by Stephen Ramsay. A listing of regex-related links is available at http://grep.extracts.de/.

=== Search examples ===

Below are some basic examples that will show you how to use MySQL regular expressions with refbase. The given links are all working examples which you can try out.

If you want to find all records where a particular person is the ''first'' author of the publication, you can prefix the person's name with a caret sign (&lt;code&gt;^&lt;/code&gt;). For example, searching the ''author'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley, ^Ackley,]

will find all records whose first author name is "Ackley". If you want to restrict the list of returned results further to only those records where a particular person is the publication's ''only'' author (i.e., has no co-authors), you may append the dollar sign (&lt;code&gt;$&lt;/code&gt;) at the end of the author's full name and initials. For example, searching for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley,%20SF$ ^Ackley, SF$]

will only find those records whose author field exactly (and only) contains the string "Ackley, SF".

Often you want to search for a particular author but you're faced with the problem that the author's name is written differently in different database records. This is often the case for authors whose names contain accented characters or umlauts. You can find all instances of an author's name by using the dot metacharacter (&lt;code&gt;.&lt;/code&gt;) which matches every character but the newline character. As an example, to find records where the ''author'' field contains "G&amp;oacute;mez" as well as "Gomez", you may use:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G.mez G.mez]

Since the dot metacharacter does not only match the characters "o" and "&amp;oacute;" but also other characters, this search would also find authors whose name is e.g. "Gimez". To avoid this, you can specify the allowed characters explicitly by enclosing them with square brackets:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G%5Bo%F3%5Dmez G&amp;#91;o&amp;oacute;&amp;#93;mez]

This will only find records whose ''author'' field contains either "Gomez" or "G&amp;oacute;mez". In the above example, the square brackets denote a so-called character class, which you can also use to specify a range of characters. The following example will find all records where the year field contains years between 2002 and 2006:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?year=200%5B2-6%5D 200&amp;#91;2-6&amp;#93;]

You can also use a negated character class by prefixing your list of characters within the square brackets with a caret sign (&lt;code&gt;^&lt;/code&gt;) &amp;#8211; which effectively matches every character that is ''not'' given within your character class. This may come in handy if you want to find an author whose name may contain more than one variable character. For example, searching for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L%5B^%20%5D%2Bnne L&amp;#91;^ &amp;#93;+nne]

will find entries where the ''author'' field contains "Lonne", "L&amp;ouml;nne", "L&amp;oslash;nne" but also "Loenne". In this example, the negated character class &lt;code&gt;[^ ]&lt;/code&gt; matches any single character that is not a space. The plus sign (&lt;code&gt;+&lt;/code&gt;) is a quantifier that allows the pattern before this quantifier to match more than once, thus matching also cases such as "Loenne". However, the above search pattern will also match author names such as "Gallienne" or "Delzenne" which may be not what you want. Again, you can specify the allowed characters more explicitly to circumvent this problem:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L(%5Bo%F6%F8%5D%7Coe)nne L(&amp;#91;o&amp;ouml;&amp;oslash;&amp;#93;&amp;#124;oe)nne]

In this example we're using grouping parentheses (&lt;code&gt;(...)&lt;/code&gt;) in combination with the alternation metacharacter (i.e. the pipe character: &lt;code&gt;|&lt;/code&gt;) which allows to match either the part within the enclosing parentheses that's left from the pipe character or the one that's right to it. In our example, the left part within the parentheses (i.e. the character class &lt;code&gt;[o&amp;ouml;&amp;oslash;]&lt;/code&gt;) will match author names such as "Lonne", "L&amp;ouml;nne" and "L&amp;oslash;nne" but not "Loenne". The right part within the parentheses (&lt;code&gt;oe&lt;/code&gt;) causes "Loenne" to be matched as well.

The dot metacharacter (&lt;code&gt;.&lt;/code&gt;) or it's repeated form (&lt;code&gt;.+&lt;/code&gt;) can be also used to find all records where the searched field isn't empty. Here's an example for the ''author'' field:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=%2E%2B .+]

Speaking of quantifiers, you can use the question mark (&lt;code&gt;?&lt;/code&gt;) which indicates that the single character (or search pattern) before the question mark is optional. This is useful when you want to search for multiple variants of a particular keyword, for example:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?keywords=pha%3Feopigment&amp;submit=Display pha?eopigment]

will find records whose ''keywords'' field contains either "phaeopigment" or "pheopigment". You can also append a question mark to a multi-character string that's enclosed by parentheses to indicate that this string is optional. For example, searching the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=bio(geo)%3Fchemistry bio(geo)?chemistry]

will find records whose title contains either "biogeochemistry" or "biochemistry".


[http://sourceforge.net/forum/forum.php?forum_id=218758 Let us know], if you've got further questions regarding the refbase search facilities.

[[Category:Usage]]</text>
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  <revision>
    <id>132</id>
    <parentid>131</parentid>
    <timestamp>2023-11-20T14:47:18Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9921" xml:space="preserve">This page explains how to use the refbase search facilities:

== Search options ==

=== Basic search ===

* [[Quick Search]]

=== Search pages ===

* [[Simple Search]]
* [[Advanced Search]]
* [[SQL Search]]
* [[Library Search]]

=== Refine your search results ===

* [[Search within Results]]
* [[SQL Search]]

=== Directly jump to particular records ===

* [[Display Details]]

=== User-specific search options ===

* [[Show My Refs]]
* [[Show My Group]]
* [[Recall My Query]]
* [[Display Details]]

== Search syntax ==

=== Basic queries ===

When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string. As an example, searching the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=arctic arctic]

will return records where the ''title'' field contains "Arctic", "Antarctic", "Antarctica", "Antarcticque" "subarctic", etc.

This "contains" search is the standard search behaviour in simple search forms such as the [[Quick Search]] or [[Search within Results]] forms. It is also used in all other search forms if "contains" or "does not contain" is selected in the drop-down that specifies the search mode.

If your search string consists of several words, refbase will return all records where the searched field literally contains the given string of words. E.g., if you searched in the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=sea%20ice%20thickness sea ice thickness]

then refbase will return any records whose title exactly contains the string "sea ice thickness". This means that you don't need to enclose a string with quotation marks to force an exact match (as is the case for various online search engines such as Google). When searching a refbase database, quotation marks are treated as regular characters and have no special meaning.

Now, what if you wanted to search a database field for the occurrence of two words which are not necessarily next to each other? In refbase, the easiest way of searching for something like "contains &lt;code&gt;xxx&lt;/code&gt; AND contains &lt;code&gt;yyy&lt;/code&gt;" is to simply start your search with the first search term (&lt;code&gt;xxx&lt;/code&gt;), then use the [[Search within Results]] form above the search results list to search for the second search term (&lt;code&gt;yyy&lt;/code&gt;). Using this method, you can quickly perform complex searches on multiple fields (and using multiple search terms) without the need of figuring out the correct search pattern in advance.

When searching for two (or more) authors of a particular paper, you often know the order in which the two authors occur. In this case you can make use of the &lt;code&gt;.+&lt;/code&gt; metacharacter sequence which matches any string of characters (more on metacharacters below). As an example, you can use:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=Cota%2E%2BSmith&amp;without=dups Cota.+Smith]

to find all records where the ''author'' field contains "Cota" followed by "Smith".

=== Using metacharacters to form complex queries ===

By default, refbase allows you to use metacharacters to describe a more complex search pattern. The deployed search syntax is called [http://en.wikipedia.org/wiki/Regular_expressions regular expressions] (often abbreviated as regexp or regex) which comes in many flavors. refbase supports MySQL regular expressions via use of the MySQL &lt;code&gt;REGEXP&lt;/code&gt; (or &lt;code&gt;RLIKE&lt;/code&gt;) syntax. The MySQL website offers an introduction on [http://dev.mysql.com/doc/refman/5.0/en/pattern-matching.html pattern matching] and provides more information about the [http://dev.mysql.com/doc/refman/5.0/en/regexp.html &lt;code&gt;REGEXP&lt;/code&gt; syntax] for regular expressions. See the examples section below for some simple usage examples.

While regular expressions provide a powerful syntax for searching they may be somewhat difficult to write and daunting if you're new to the concept of regular expressions. There are various [http://directory.google.com/Top/Computers/Programming/Languages/Regular_Expressions/FAQs,_Help,_and_Tutorials/ tutorials on regular expressions] on the net that can help you getting started. A nice [http://etext.lib.virginia.edu/helpsheets/regex.html basic introduction to regular expressions] was written by Stephen Ramsay. A listing of regex-related links is available at http://grep.extracts.de/.

=== Search examples ===

Below are some basic examples that will show you how to use MySQL regular expressions with refbase. The given links are all working examples which you can try out.

If you want to find all records where a particular person is the ''first'' author of the publication, you can prefix the person's name with a caret sign (&lt;code&gt;^&lt;/code&gt;). For example, searching the ''author'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley, ^Ackley,]

will find all records whose first author name is "Ackley". If you want to restrict the list of returned results further to only those records where a particular person is the publication's ''only'' author (i.e., has no co-authors), you may append the dollar sign (&lt;code&gt;$&lt;/code&gt;) at the end of the author's full name and initials. For example, searching for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley,%20SF$ ^Ackley, SF$]

will only find those records whose author field exactly (and only) contains the string "Ackley, SF".

Often you want to search for a particular author but you're faced with the problem that the author's name is written differently in different database records. This is often the case for authors whose names contain accented characters or umlauts. You can find all instances of an author's name by using the dot metacharacter (&lt;code&gt;.&lt;/code&gt;) which matches every character but the newline character. As an example, to find records where the ''author'' field contains "G&amp;oacute;mez" as well as "Gomez", you may use:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G.mez G.mez]

Since the dot metacharacter does not only match the characters "o" and "&amp;oacute;" but also other characters, this search would also find authors whose name is e.g. "Gimez". To avoid this, you can specify the allowed characters explicitly by enclosing them with square brackets:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G%5Bo%F3%5Dmez G&amp;#91;o&amp;oacute;&amp;#93;mez]

This will only find records whose ''author'' field contains either "Gomez" or "G&amp;oacute;mez". In the above example, the square brackets denote a so-called character class, which you can also use to specify a range of characters. The following example will find all records where the year field contains years between 2002 and 2006:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?year=200%5B2-6%5D 200&amp;#91;2-6&amp;#93;]

You can also use a negated character class by prefixing your list of characters within the square brackets with a caret sign (&lt;code&gt;^&lt;/code&gt;) &amp;#8211; which effectively matches every character that is ''not'' given within your character class. This may come in handy if you want to find an author whose name may contain more than one variable character. For example, searching for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L%5B^%20%5D%2Bnne L&amp;#91;^ &amp;#93;+nne]

will find entries where the ''author'' field contains "Lonne", "L&amp;ouml;nne", "L&amp;oslash;nne" but also "Loenne". In this example, the negated character class &lt;code&gt;[^ ]&lt;/code&gt; matches any single character that is not a space. The plus sign (&lt;code&gt;+&lt;/code&gt;) is a quantifier that allows the pattern before this quantifier to match more than once, thus matching also cases such as "Loenne". However, the above search pattern will also match author names such as "Gallienne" or "Delzenne" which may be not what you want. Again, you can specify the allowed characters more explicitly to circumvent this problem:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L(%5Bo%F6%F8%5D%7Coe)nne L(&amp;#91;o&amp;ouml;&amp;oslash;&amp;#93;&amp;#124;oe)nne]

In this example we're using grouping parentheses (&lt;code&gt;(...)&lt;/code&gt;) in combination with the alternation metacharacter (i.e. the pipe character: &lt;code&gt;|&lt;/code&gt;) which allows to match either the part within the enclosing parentheses that's left from the pipe character or the one that's right to it. In our example, the left part within the parentheses (i.e. the character class &lt;code&gt;[o&amp;ouml;&amp;oslash;]&lt;/code&gt;) will match author names such as "Lonne", "L&amp;ouml;nne" and "L&amp;oslash;nne" but not "Loenne". The right part within the parentheses (&lt;code&gt;oe&lt;/code&gt;) causes "Loenne" to be matched as well.

The dot metacharacter (&lt;code&gt;.&lt;/code&gt;) or it's repeated form (&lt;code&gt;.+&lt;/code&gt;) can be also used to find all records where the searched field isn't empty. Here's an example for the ''author'' field:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=%2E%2B .+]

Speaking of quantifiers, you can use the question mark (&lt;code&gt;?&lt;/code&gt;) which indicates that the single character (or search pattern) before the question mark is optional. This is useful when you want to search for multiple variants of a particular keyword, for example:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?keywords=pha%3Feopigment&amp;submit=Display pha?eopigment]

will find records whose ''keywords'' field contains either "phaeopigment" or "pheopigment". You can also append a question mark to a multi-character string that's enclosed by parentheses to indicate that this string is optional. For example, searching the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=bio(geo)%3Fchemistry bio(geo)?chemistry]

will find records whose title contains either "biogeochemistry" or "biochemistry".


[http://sourceforge.net/forum/forum.php?forum_id=218758 Let us know], if you've got further questions regarding the refbase search facilities.

[[Category:Usage]]
__NOEDITSECTION__</text>
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  <revision>
    <id>133</id>
    <parentid>132</parentid>
    <timestamp>2023-11-20T15:20:43Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update external links (TODO: appropriate replacements for https://refbase.ipoe.uni-kiel.de links)</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="9820" xml:space="preserve">This page explains how to use the refbase search facilities:

== Search options ==

=== Basic search ===

* [[Quick Search]]

=== Search pages ===

* [[Simple Search]]
* [[Advanced Search]]
* [[SQL Search]]
* [[Library Search]]

=== Refine your search results ===

* [[Search within Results]]
* [[SQL Search]]

=== Directly jump to particular records ===

* [[Display Details]]

=== User-specific search options ===

* [[Show My Refs]]
* [[Show My Group]]
* [[Recall My Query]]
* [[Display Details]]

== Search syntax ==

=== Basic queries ===

When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string. As an example, searching the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=arctic arctic]

will return records where the ''title'' field contains "Arctic", "Antarctic", "Antarctica", "Antarcticque" "subarctic", etc.

This "contains" search is the standard search behaviour in simple search forms such as the [[Quick Search]] or [[Search within Results]] forms. It is also used in all other search forms if "contains" or "does not contain" is selected in the drop-down that specifies the search mode.

If your search string consists of several words, refbase will return all records where the searched field literally contains the given string of words. E.g., if you searched in the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=sea%20ice%20thickness sea ice thickness]

then refbase will return any records whose title exactly contains the string "sea ice thickness". This means that you don't need to enclose a string with quotation marks to force an exact match (as is the case for various online search engines such as Google). When searching a refbase database, quotation marks are treated as regular characters and have no special meaning.

Now, what if you wanted to search a database field for the occurrence of two words which are not necessarily next to each other? In refbase, the easiest way of searching for something like "contains &lt;code&gt;xxx&lt;/code&gt; AND contains &lt;code&gt;yyy&lt;/code&gt;" is to simply start your search with the first search term (&lt;code&gt;xxx&lt;/code&gt;), then use the [[Search within Results]] form above the search results list to search for the second search term (&lt;code&gt;yyy&lt;/code&gt;). Using this method, you can quickly perform complex searches on multiple fields (and using multiple search terms) without the need of figuring out the correct search pattern in advance.

When searching for two (or more) authors of a particular paper, you often know the order in which the two authors occur. In this case you can make use of the &lt;code&gt;.+&lt;/code&gt; metacharacter sequence which matches any string of characters (more on metacharacters below). As an example, you can use:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=Cota%2E%2BSmith&amp;without=dups Cota.+Smith]

to find all records where the ''author'' field contains "Cota" followed by "Smith".

=== Using metacharacters to form complex queries ===

By default, refbase allows you to use metacharacters to describe a more complex search pattern. The deployed search syntax is called [http://en.wikipedia.org/wiki/Regular_expressions regular expressions] (often abbreviated as regexp or regex) which comes in many flavors. refbase supports MySQL regular expressions via use of the MySQL &lt;code&gt;REGEXP&lt;/code&gt; (or &lt;code&gt;RLIKE&lt;/code&gt;) syntax. The MySQL website offers an introduction on [https://dev.mysql.com/doc/refman/8.0/en/pattern-matching.html pattern matching] and provides more information about the [https://dev.mysql.com/doc/refman/8.0/en/regexp.html &lt;code&gt;REGEXP&lt;/code&gt; syntax] for regular expressions. See the examples section below for some simple usage examples.

While regular expressions provide a powerful syntax for searching they may be somewhat difficult to write and daunting if you're new to the concept of regular expressions. There are various [https://www.google.com/search?q=regular+expressions+tutorial tutorials on regular expressions] on the net that can help you getting started. A nice [http://linuxclass.heinz.cmu.edu/doc/regex.html basic introduction to regular expressions] ([https://solaris-8.tripod.com/regexp.pdf PDF version]) was written by Stephen Ramsay.

=== Search examples ===

Below are some basic examples that will show you how to use MySQL regular expressions with refbase. The given links are all working examples which you can try out.

If you want to find all records where a particular person is the ''first'' author of the publication, you can prefix the person's name with a caret sign (&lt;code&gt;^&lt;/code&gt;). For example, searching the ''author'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley, ^Ackley,]

will find all records whose first author name is "Ackley". If you want to restrict the list of returned results further to only those records where a particular person is the publication's ''only'' author (i.e., has no co-authors), you may append the dollar sign (&lt;code&gt;$&lt;/code&gt;) at the end of the author's full name and initials. For example, searching for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=^Ackley,%20SF$ ^Ackley, SF$]

will only find those records whose author field exactly (and only) contains the string "Ackley, SF".

Often you want to search for a particular author but you're faced with the problem that the author's name is written differently in different database records. This is often the case for authors whose names contain accented characters or umlauts. You can find all instances of an author's name by using the dot metacharacter (&lt;code&gt;.&lt;/code&gt;) which matches every character but the newline character. As an example, to find records where the ''author'' field contains "G&amp;oacute;mez" as well as "Gomez", you may use:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G.mez G.mez]

Since the dot metacharacter does not only match the characters "o" and "&amp;oacute;" but also other characters, this search would also find authors whose name is e.g. "Gimez". To avoid this, you can specify the allowed characters explicitly by enclosing them with square brackets:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=G%5Bo%F3%5Dmez G&amp;#91;o&amp;oacute;&amp;#93;mez]

This will only find records whose ''author'' field contains either "Gomez" or "G&amp;oacute;mez". In the above example, the square brackets denote a so-called character class, which you can also use to specify a range of characters. The following example will find all records where the year field contains years between 2002 and 2006:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?year=200%5B2-6%5D 200&amp;#91;2-6&amp;#93;]

You can also use a negated character class by prefixing your list of characters within the square brackets with a caret sign (&lt;code&gt;^&lt;/code&gt;) &amp;#8211; which effectively matches every character that is ''not'' given within your character class. This may come in handy if you want to find an author whose name may contain more than one variable character. For example, searching for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L%5B^%20%5D%2Bnne L&amp;#91;^ &amp;#93;+nne]

will find entries where the ''author'' field contains "Lonne", "L&amp;ouml;nne", "L&amp;oslash;nne" but also "Loenne". In this example, the negated character class &lt;code&gt;[^ ]&lt;/code&gt; matches any single character that is not a space. The plus sign (&lt;code&gt;+&lt;/code&gt;) is a quantifier that allows the pattern before this quantifier to match more than once, thus matching also cases such as "Loenne". However, the above search pattern will also match author names such as "Gallienne" or "Delzenne" which may be not what you want. Again, you can specify the allowed characters more explicitly to circumvent this problem:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=L(%5Bo%F6%F8%5D%7Coe)nne L(&amp;#91;o&amp;ouml;&amp;oslash;&amp;#93;&amp;#124;oe)nne]

In this example we're using grouping parentheses (&lt;code&gt;(...)&lt;/code&gt;) in combination with the alternation metacharacter (i.e. the pipe character: &lt;code&gt;|&lt;/code&gt;) which allows to match either the part within the enclosing parentheses that's left from the pipe character or the one that's right to it. In our example, the left part within the parentheses (i.e. the character class &lt;code&gt;[o&amp;ouml;&amp;oslash;]&lt;/code&gt;) will match author names such as "Lonne", "L&amp;ouml;nne" and "L&amp;oslash;nne" but not "Loenne". The right part within the parentheses (&lt;code&gt;oe&lt;/code&gt;) causes "Loenne" to be matched as well.

The dot metacharacter (&lt;code&gt;.&lt;/code&gt;) or it's repeated form (&lt;code&gt;.+&lt;/code&gt;) can be also used to find all records where the searched field isn't empty. Here's an example for the ''author'' field:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?author=%2E%2B .+]

Speaking of quantifiers, you can use the question mark (&lt;code&gt;?&lt;/code&gt;) which indicates that the single character (or search pattern) before the question mark is optional. This is useful when you want to search for multiple variants of a particular keyword, for example:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?keywords=pha%3Feopigment&amp;submit=Display pha?eopigment]

will find records whose ''keywords'' field contains either "phaeopigment" or "pheopigment". You can also append a question mark to a multi-character string that's enclosed by parentheses to indicate that this string is optional. For example, searching the ''title'' field for:

 [https://refbase.ipoe.uni-kiel.de/refs/show.php?title=bio(geo)%3Fchemistry bio(geo)?chemistry]

will find records whose title contains either "biogeochemistry" or "biochemistry".


[[refbase:Community_portal|Let us know]] if you've got further questions regarding the refbase search facilities.

[[Category:Usage]]
__NOEDITSECTION__</text>
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</page>
<page arvcontinue="20231106215615|104">
  <title>Editing records</title>
  <ns>0</ns>
  <id>42</id>
  <revision>
    <id>134</id>
    <timestamp>2023-11-20T15:36:54Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <comment>Original page content from 23-Oct-2006</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2359" xml:space="preserve">== General notes about editing ==

We strongly believe in the '''[http://en.wikipedia.org/wiki/Wiki wiki] approach of collaboration''' where every (logged-in) user is allowed to edit every database record. Normally, this tremendeously helps to improve the quality of your records since everybody can easily make corrections and/or additions. Actually, we have never heard of any serious misuse of this feature.

Of course, there may be some valid concerns among your users about data persistence. When discussing this issue with your users, it's worth pointing out these things:

* While the basic bibliographic data of a record are shared among users (and can be edited by every user), every user has in fact private, i.e., '''user-specific fields''' that nobody else can view. These are the "yellow" fields at the bottom of each entry when viewed in details view. People can put their private keys and notes there without having to fear that somebody else will read them.

* refbase allows users to setup (and subscribe to) custom '''RSS feeds''' that '''track''' any '''changes''' made to records that belong to their own library.

* It should be relatively easy to setup a cron job on your '''server''' that '''backups''' the refbase database at regular intervals, say, every night. An example for a backup script is given [[Backup_the_database|here]].

: This ensures that you can retrieve a previous version of a particular record in case some malicious user did something bad. And with a rigorous backup strategy on the server, this setup may already be much safer than most people's own literature database on their local machine.

* It's also worth pointing out that every user can '''install refbase locally''' &amp;ndash; provided the user has a webserver installed. But with projects such as [http://www.xampp.org/ XAMPP], this has become very easy.

: The backup dump file that you get from the [[Backup_the_database#mysqldump|mysqldump]] utility can be used as base data file when installing refbase. This means, that users could grab a recent backup copy of your refbase database from your server (if you allow them to do so) and install it locally on their machine for convenient '''offline access'''. The same method can be used to update a local copy of a refbase database with updated data from the server's master database.

[[Category:Usage]]</text>
    <sha1>6d33632ed170be821148161a60701667b10519a4</sha1>
  </revision>
  <revision>
    <id>135</id>
    <parentid>134</parentid>
    <timestamp>2023-11-20T15:37:29Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2377" xml:space="preserve">== General notes about editing ==

We strongly believe in the '''[http://en.wikipedia.org/wiki/Wiki wiki] approach of collaboration''' where every (logged-in) user is allowed to edit every database record. Normally, this tremendeously helps to improve the quality of your records since everybody can easily make corrections and/or additions. Actually, we have never heard of any serious misuse of this feature.

Of course, there may be some valid concerns among your users about data persistence. When discussing this issue with your users, it's worth pointing out these things:

* While the basic bibliographic data of a record are shared among users (and can be edited by every user), every user has in fact private, i.e., '''user-specific fields''' that nobody else can view. These are the "yellow" fields at the bottom of each entry when viewed in details view. People can put their private keys and notes there without having to fear that somebody else will read them.

* refbase allows users to setup (and subscribe to) custom '''RSS feeds''' that '''track''' any '''changes''' made to records that belong to their own library.

* It should be relatively easy to setup a cron job on your '''server''' that '''backups''' the refbase database at regular intervals, say, every night. An example for a backup script is given [[Backup_the_database|here]].

: This ensures that you can retrieve a previous version of a particular record in case some malicious user did something bad. And with a rigorous backup strategy on the server, this setup may already be much safer than most people's own literature database on their local machine.

* It's also worth pointing out that every user can '''install refbase locally''' &amp;ndash; provided the user has a webserver installed. But with projects such as [http://www.xampp.org/ XAMPP], this has become very easy.

: The backup dump file that you get from the [[Backup_the_database#mysqldump|mysqldump]] utility can be used as base data file when installing refbase. This means, that users could grab a recent backup copy of your refbase database from your server (if you allow them to do so) and install it locally on their machine for convenient '''offline access'''. The same method can be used to update a local copy of a refbase database with updated data from the server's master database.

[[Category:Usage]]
__NOEDITSECTION__</text>
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  <revision>
    <id>136</id>
    <parentid>135</parentid>
    <timestamp>2023-11-20T15:38:43Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Update external links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="2386" xml:space="preserve">== General notes about editing ==

We strongly believe in the '''[http://en.wikipedia.org/wiki/Wiki wiki] approach of collaboration''' where every (logged-in) user is allowed to edit every database record. Normally, this tremendeously helps to improve the quality of your records since everybody can easily make corrections and/or additions. Actually, we have never heard of any serious misuse of this feature.

Of course, there may be some valid concerns among your users about data persistence. When discussing this issue with your users, it's worth pointing out these things:

* While the basic bibliographic data of a record are shared among users (and can be edited by every user), every user has in fact private, i.e., '''user-specific fields''' that nobody else can view. These are the "yellow" fields at the bottom of each entry when viewed in details view. People can put their private keys and notes there without having to fear that somebody else will read them.

* refbase allows users to setup (and subscribe to) custom '''RSS feeds''' that '''track''' any '''changes''' made to records that belong to their own library.

* It should be relatively easy to setup a cron job on your '''server''' that '''backups''' the refbase database at regular intervals, say, every night. An example for a backup script is given [[Backup_the_database|here]].

: This ensures that you can retrieve a previous version of a particular record in case some malicious user did something bad. And with a rigorous backup strategy on the server, this setup may already be much safer than most people's own literature database on their local machine.

* It's also worth pointing out that every user can '''install refbase locally''' &amp;ndash; provided the user has a webserver installed. But with projects such as [https://www.apachefriends.org/ XAMPP], this has become very easy.

: The backup dump file that you get from the [[Backup_the_database#mysqldump|mysqldump]] utility can be used as base data file when installing refbase. This means, that users could grab a recent backup copy of your refbase database from your server (if you allow them to do so) and install it locally on their machine for convenient '''offline access'''. The same method can be used to update a local copy of a refbase database with updated data from the server's master database.

[[Category:Usage]]
__NOEDITSECTION__</text>
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<page arvcontinue="20231106215615|104">
  <title>Adding records</title>
  <ns>0</ns>
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  <revision>
    <id>137</id>
    <timestamp>2023-11-20T15:56:00Z</timestamp>
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    <comment>Original page content from 20-Mar-2012</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6449" xml:space="preserve">== General requirement for adding records ==

*as default, one has to be logged in to edit an record. This default can be changed from the admin
*the ''add record''-page has to be opened. This can be easily done at with the link at the header of every page
*some browsers (e.g. firefox) have problems with pasting in text with line breaks. So please remove line breaks before pasting the text in these cases.

== General description of the ''Add Record'' page ==

*you will see several input-fields, which are grouped. Groups are indicated by color-coding (colors may vary with used browser, used stylesheets etc.)
#grey fields:
#*such as ''author'', ''title'', ''year'' and ''publication''
#*these are mandatory fields, which are necessary for correct citation of references
#white fields:
#*such as ''abstract'', ''keywords'' and ''ISBN''
#*these are facultative fields, which are not necessary for correct citation
#*but these fields will give a additional benifit to your database, for searching abstracts etc.
#yellow fields:
#*such as ''marked'', ''user keys'' and ''related''
#*these fields are facultative fields, which are '''only visible for the logged in user'''
#*this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

the author(s) of the publication
*several authors separated by semicolon (;)
*surname and '''forename(s)''' or forename-initials separated by comma (,)
*no points and no space character between forename-initials

Note that you should decide whether you'd like to use fully written fornames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

 example: Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is Editor
*please activate, if persons, entered in ''author''-field are editors of the publication
*only relevant for books (Type: "''book whole''")

==== Title ====

the title of the publication
*no dot at the end
*species-names can be set as '''italic''' by surrounding by underscore
*use "[super:...]" to impose words
*use "[sub:...]" to lower words
 examples:
 Feeding of _Sprattus sprattus_ in the Baltic Sea
 Decomposition of [super:14]C-labelled glucose
 Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

defines the type of the publication
*simply select an item from drop-down-list
*'''this entry is used for defining the citation style of the publication'''. Therefore selection should be made carfully
*this entry defines visibility of related files (e.g. .pdf). As default, for publications of Type="''Thesis''" the files are visible for not logged in users, as well 
*see [[Configuring refbase|configuration of refbase]] to learn how to add/remove entries in the list

==== Year ====

the year of the publication
*enter in four-digit-style
 example: 2003

==== Publication ====

complete name of publication
*insert here the complete (!) name of the Journal (if Type=''Journal Article'') or of the book (if Type=''Book Chapter'')
*abbreviated Jounal-names has to be entered in the field "''Abbrev Jounal''"
*'''a list of journal-names and -abbreviations (related to aquatic sciences) can be found by open ''journals.php'' in the root directory of the refbase URL'''
 examples:
 Canadian Journal of Fisheries and Aquatic Sciences
 The northern North Atlantic: A changing environment

==== Abbrev Journal ====

the abbreviated name of the publication
*enter the abbreviated journal-name without dots
*'''a list of journal-names and -abbreviations (related to aquatic sciences) can be found by open ''journals.php'' in the root directory of the refbase URL'''
 example:
 Can J Fish Aquat Sci

==== Volume ====

the volume of the publication
 example: 245

==== Issue ====

the issue of a publication within a volume
*often a ''Volume'' of a journal consist of several issues
*the single booklet is called ''Issue'' and is labelled by a number
 examples: 3 ''or'' C2
  
==== Pages ====

defines which pages of the publication are covered with the reference
*enter '''range of pages''', when using Types "''Journal Articles''" and "''Book Chapter''"
*enter '''total number of pages''' including "''pp''" (without dot) when using Types"''Book Whole''" and "''Manuscript''"
 examples:
 12 (article has only one page)
 35-42 (article or book chapter starts at page 35 and ends at page 42)
 620 pp (book has 620 pages in total)

=== Facultative fields (white fields) ===

==== Corporate Author ====

the institution or society to which so the author is associated
*defines the institution under which the author published his work
*for Diploma- or Phd-thesis this would be the name of the university/department
 example: Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

the type of a thesis
*if the publication is a thesis, this field defines the type of academic degree
*see [[Configuring refbase|configuration of refbase]] to learn how to add/remove entries in the list
 examples: diploma thesis, Ph.D.thesis, Doctoral thesis, Habilitation thesis

==== Adress ====

the adress of the authors
*contains contact informations, how to contact the authors (in most cases the first author) of the paper (e.g. postal adress, Fax, email et.)
 example:
 Granskog: Department of Geophysics, P.O. Box 64, FIN-00014
 University of Helsinki, Finland, Email: mats@iki.fi;
 Meiners: Institute for Polar Ecology, University of Kiel,
 Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

the keywords given by the author
*contains keywords, as given in the article
*your personal keywords can be entered under [[Adding Records#User Keys|User Keys]]
*multiple items should be seperated by semicolon (";")
 examples:
 Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

the abstract for this publication (if any)as given by the author
*some browsers (e.g. firefox) have problems with pasting in text with line breaks. So please remove line breaks before pasting the text in these cases.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

[[Category:Usage]]</text>
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  </revision>
  <revision>
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    <minor/>
    <comment>Hide section edit links</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6467" xml:space="preserve">== General requirement for adding records ==

*as default, one has to be logged in to edit an record. This default can be changed from the admin
*the ''add record''-page has to be opened. This can be easily done at with the link at the header of every page
*some browsers (e.g. firefox) have problems with pasting in text with line breaks. So please remove line breaks before pasting the text in these cases.

== General description of the ''Add Record'' page ==

*you will see several input-fields, which are grouped. Groups are indicated by color-coding (colors may vary with used browser, used stylesheets etc.)
#grey fields:
#*such as ''author'', ''title'', ''year'' and ''publication''
#*these are mandatory fields, which are necessary for correct citation of references
#white fields:
#*such as ''abstract'', ''keywords'' and ''ISBN''
#*these are facultative fields, which are not necessary for correct citation
#*but these fields will give a additional benifit to your database, for searching abstracts etc.
#yellow fields:
#*such as ''marked'', ''user keys'' and ''related''
#*these fields are facultative fields, which are '''only visible for the logged in user'''
#*this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

the author(s) of the publication
*several authors separated by semicolon (;)
*surname and '''forename(s)''' or forename-initials separated by comma (,)
*no points and no space character between forename-initials

Note that you should decide whether you'd like to use fully written fornames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

 example: Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is Editor
*please activate, if persons, entered in ''author''-field are editors of the publication
*only relevant for books (Type: "''book whole''")

==== Title ====

the title of the publication
*no dot at the end
*species-names can be set as '''italic''' by surrounding by underscore
*use "[super:...]" to impose words
*use "[sub:...]" to lower words
 examples:
 Feeding of _Sprattus sprattus_ in the Baltic Sea
 Decomposition of [super:14]C-labelled glucose
 Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

defines the type of the publication
*simply select an item from drop-down-list
*'''this entry is used for defining the citation style of the publication'''. Therefore selection should be made carfully
*this entry defines visibility of related files (e.g. .pdf). As default, for publications of Type="''Thesis''" the files are visible for not logged in users, as well 
*see [[Configuring refbase|configuration of refbase]] to learn how to add/remove entries in the list

==== Year ====

the year of the publication
*enter in four-digit-style
 example: 2003

==== Publication ====

complete name of publication
*insert here the complete (!) name of the Journal (if Type=''Journal Article'') or of the book (if Type=''Book Chapter'')
*abbreviated Jounal-names has to be entered in the field "''Abbrev Jounal''"
*'''a list of journal-names and -abbreviations (related to aquatic sciences) can be found by open ''journals.php'' in the root directory of the refbase URL'''
 examples:
 Canadian Journal of Fisheries and Aquatic Sciences
 The northern North Atlantic: A changing environment

==== Abbrev Journal ====

the abbreviated name of the publication
*enter the abbreviated journal-name without dots
*'''a list of journal-names and -abbreviations (related to aquatic sciences) can be found by open ''journals.php'' in the root directory of the refbase URL'''
 example:
 Can J Fish Aquat Sci

==== Volume ====

the volume of the publication
 example: 245

==== Issue ====

the issue of a publication within a volume
*often a ''Volume'' of a journal consist of several issues
*the single booklet is called ''Issue'' and is labelled by a number
 examples: 3 ''or'' C2
  
==== Pages ====

defines which pages of the publication are covered with the reference
*enter '''range of pages''', when using Types "''Journal Articles''" and "''Book Chapter''"
*enter '''total number of pages''' including "''pp''" (without dot) when using Types"''Book Whole''" and "''Manuscript''"
 examples:
 12 (article has only one page)
 35-42 (article or book chapter starts at page 35 and ends at page 42)
 620 pp (book has 620 pages in total)

=== Facultative fields (white fields) ===

==== Corporate Author ====

the institution or society to which so the author is associated
*defines the institution under which the author published his work
*for Diploma- or Phd-thesis this would be the name of the university/department
 example: Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

the type of a thesis
*if the publication is a thesis, this field defines the type of academic degree
*see [[Configuring refbase|configuration of refbase]] to learn how to add/remove entries in the list
 examples: diploma thesis, Ph.D.thesis, Doctoral thesis, Habilitation thesis

==== Adress ====

the adress of the authors
*contains contact informations, how to contact the authors (in most cases the first author) of the paper (e.g. postal adress, Fax, email et.)
 example:
 Granskog: Department of Geophysics, P.O. Box 64, FIN-00014
 University of Helsinki, Finland, Email: mats@iki.fi;
 Meiners: Institute for Polar Ecology, University of Kiel,
 Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

the keywords given by the author
*contains keywords, as given in the article
*your personal keywords can be entered under [[Adding Records#User Keys|User Keys]]
*multiple items should be seperated by semicolon (";")
 examples:
 Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

the abstract for this publication (if any)as given by the author
*some browsers (e.g. firefox) have problems with pasting in text with line breaks. So please remove line breaks before pasting the text in these cases.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

[[Category:Usage]]
__NOEDITSECTION__</text>
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  </revision>
  <revision>
    <id>140</id>
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    <timestamp>2023-11-20T17:26:24Z</timestamp>
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    <comment>Updates formatting &amp; case, removes outdated info and fixes some typos</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6019" xml:space="preserve">== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.
* Open the ''Add record'' page by clicking the link at the top of every page.

== General description of the ''Add Record'' page ==

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (&lt;code&gt;;&lt;/code&gt;)
* Separate  surname and forename(s) ( or forename initials) by a comma (&lt;code&gt;,&lt;/code&gt;)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

 Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with &lt;code&gt;[super:...]&lt;/code&gt; will cause them to appear above the normal text baseline.
* Wrapping subscript letters with &lt;code&gt;[sub:...]&lt;/code&gt; will cause them to appear below the normal text baseline.

Examples:

 Feeding of _Sprattus sprattus_ in the Baltic Sea
 Decomposition of [super:14]C-labelled glucose
 Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

 2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

 Canadian Journal of Fisheries and Aquatic Sciences
 The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

 Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

 245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

 3
 C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

 12      ''-&gt; article has only one page''
 35-42   ''-&gt; article or book chapter starts at page 35 and ends at page 42''
 620 pp  ''-&gt; book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

 Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

 diploma thesis
 Ph.D.thesis
 Doctoral thesis
 Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

 Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
 Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding Records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (&lt;code&gt;;&lt;/code&gt;).

Examples:

 Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

[[Category:Usage]]
__NOEDITSECTION__</text>
    <sha1>5f2110532c41629bfb9b636645e675217d7c1b3c</sha1>
  </revision>
  <revision>
    <id>141</id>
    <parentid>140</parentid>
    <timestamp>2023-11-20T17:27:30Z</timestamp>
    <contributor>
      <username>WikiSysop</username>
      <id>1</id>
    </contributor>
    <minor/>
    <comment>Fix internal link</comment>
    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="6019" xml:space="preserve">== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.
* Open the ''Add record'' page by clicking the link at the top of every page.

== General description of the ''Add Record'' page ==

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (&lt;code&gt;;&lt;/code&gt;)
* Separate  surname and forename(s) ( or forename initials) by a comma (&lt;code&gt;,&lt;/code&gt;)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

 Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with &lt;code&gt;[super:...]&lt;/code&gt; will cause them to appear above the normal text baseline.
* Wrapping subscript letters with &lt;code&gt;[sub:...]&lt;/code&gt; will cause them to appear below the normal text baseline.

Examples:

 Feeding of _Sprattus sprattus_ in the Baltic Sea
 Decomposition of [super:14]C-labelled glucose
 Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

 2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

 Canadian Journal of Fisheries and Aquatic Sciences
 The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

 Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

 245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

 3
 C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

 12      ''-&gt; article has only one page''
 35-42   ''-&gt; article or book chapter starts at page 35 and ends at page 42''
 620 pp  ''-&gt; book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

 Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

 diploma thesis
 Ph.D.thesis
 Doctoral thesis
 Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

 Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
 Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding_records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (&lt;code&gt;;&lt;/code&gt;).

Examples:

 Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

[[Category:Usage]]
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    <text bytes="7064" xml:space="preserve">== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.
* Open the ''Add record'' page by clicking the link at the top of every page.

== General description of the ''Add Record'' page ==

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (&lt;code&gt;;&lt;/code&gt;)
* Separate  surname and forename(s) ( or forename initials) by a comma (&lt;code&gt;,&lt;/code&gt;)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

 Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with &lt;code&gt;[super:...]&lt;/code&gt; will cause them to appear above the normal text baseline.
* Wrapping subscript letters with &lt;code&gt;[sub:...]&lt;/code&gt; will cause them to appear below the normal text baseline.

Examples:

 Feeding of _Sprattus sprattus_ in the Baltic Sea
 Decomposition of [super:14]C-labelled glucose
 Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

 2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

 Canadian Journal of Fisheries and Aquatic Sciences
 The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

 Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

 245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

 3
 C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

 12      ''-&gt; article has only one page''
 35-42   ''-&gt; article or book chapter starts at page 35 and ends at page 42''
 620 pp  ''-&gt; book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

 Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

 diploma thesis
 Ph.D.thesis
 Doctoral thesis
 Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

 Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
 Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding_records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (&lt;code&gt;;&lt;/code&gt;).

Examples:

 Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

==== Marked &amp; Selected ====

* Both fields can be used to permanently "mark" (or "select") records so that one can easily come back to these records later on. It's up to you how you use these fields.
* The "selected" field is meant to indicate your "selected publications". This can be used to easily gather all publications of a particular author that shall be included on the institute's web site. Here's an example:

 [http://polaris.ipoe.uni-kiel.de/refs/show.php?author=piepenburg,%20d&amp;userID=4&amp;selected=yes&amp;submit=Cite&amp;showRows=100&amp;citeOrder=year&amp;headerMsg=Publications%20of%20**Dieter%20Piepenburg**: Publications of Dieter Piepenburg]

: In the above URL, note the use of the &lt;code&gt;&amp;selected=yes&lt;/code&gt; bit. I.e. the above URL displays all selected records that were authored by "D. Piepenburg" in Citation view (grouped by publication year), and adds a header message above the results list.

: For more info, please see how to setup dynamically updating [[Auto-updating_author/group_bibliographies|author (or group) bibliographies]].

[[Category:Usage]]
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="7063" xml:space="preserve">== General requirement for adding records ==

* By default, one has to be logged in to edit a record. This default can be changed by the admin.

== General description of the ''Add Record'' page ==

Open the ''Add record'' page by clicking the link at the top of every page.

* The ''Add record'' page has several input fields, which are grouped. Groups are indicated by color coding:
# Grey fields:
#* e.g. ''author'', ''title'', ''year'' and ''publication''
#* these are mandatory fields, which are necessary for correct citation of references
# White fields:
#* e.g. ''abstract'', ''keywords'' and ''ISBN''
#* these are facultative fields, which are not necessary for correct citation
#* however, filling these fields will be beneficial for your database users, e.g. when searching abstracts
# Yellow fields:
#* e.g. ''marked'', ''user keys'' and ''related''
#* these fields are facultative fields, which are '''only visible for the logged in user'''
#* this allows a personalization of a common used references

== Filling the fields ==

Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the [[Table refs|''refs'']] MySQL table.

=== Mandatory fields (grey fields) ===

==== Author ====

The author(s) of the publication.
* Separate multiple authors by a semicolon (&lt;code&gt;;&lt;/code&gt;)
* Separate  surname and forename(s) ( or forename initials) by a comma (&lt;code&gt;,&lt;/code&gt;)
* No space character between forename initials

Note that you should decide whether you'd like to use fully written forenames or initials and apply this rule to all of your database records. When citing records, correct sorting of records is only possible if ''all'' cited records have either fully written forenames or just initials.

Example:

 Granskog,MA; Virkanen, J

==== is Editor ====

'''Yes''' if author is editor.
* Mark this field if persons entered in the ''author'' field are actually editors of the publication.
* Only relevant for books (type "''book whole''").

==== Title ====

The title of the publication.
* No dot at the end.
* Species or ship name(s) can be set in ''italics'' by surrounding the name(s) with underscores.
* Wrapping superscript letters with &lt;code&gt;[super:...]&lt;/code&gt; will cause them to appear above the normal text baseline.
* Wrapping subscript letters with &lt;code&gt;[sub:...]&lt;/code&gt; will cause them to appear below the normal text baseline.

Examples:

 Feeding of _Sprattus sprattus_ in the Baltic Sea
 Decomposition of [super:14]C-labelled glucose
 Factors controlling CaCO[sub:2] dissolution in the Weddell Sea

==== Type ====

Defines the type of the publication.
* Simply select an item from the drop-down list.
* Note that the publication type will influence the visibility of related files (e.g. .pdf files). By default, for publications of type "''Thesis''", attached files are also visible for not-logged in users.

==== Year ====

The year of the publication.
* Enter years in four-digit style.

Example:

 2003

==== Publication ====

The complete name of the publication.
* Insert here the complete name of the Journal (if type ''Journal Article'') or book (if type ''Book Chapter'').
* Abbreviated jounal names should be entered in the "''Abbrev Jounal''" field.

Examples:

 Canadian Journal of Fisheries and Aquatic Sciences
 The northern North Atlantic: A changing environment

==== Abbrev Journal ====

The abbreviated name of the publication.
* For a list of journal names and its abbreviations, see e.g. [https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html Web of Science] or [https://ftp.ncbi.nih.gov/pubmed/J_Medline.txt PubMed].

Example:

 Can J Fish Aquat Sci

==== Volume ====

The volume of the publication.

Example:

 245

==== Issue ====

The issue of a publication within a volume.
* Often, a ''Volume'' of a journal consists of several issues.
* An ''Issue'' is a single booklet and is labelled by a number.

Examples:

 3
 C2

==== Pages ====

Defines which pages of the publication are covered by the reference.
* Enter a '''range of pages''', when using types "''Journal Article''" and "''Book Chapter''".
* Enter the '''total number of pages''' including "''pp''" (without any dots) when using types "''Book Whole''" and "''Manuscript''".

Examples:

 12      ''-&gt; article has only one page''
 35-42   ''-&gt; article or book chapter starts at page 35 and ends at page 42''
 620 pp  ''-&gt; book has 620 pages in total''

=== Facultative fields (white fields) ===

==== Corporate Author ====

The institution or society associated with the author.
* Usually the institution under which the author published his/her work.
* For Diploma or Phd theses, this would be the name of the university/department.

Example:

 Leibniz-Institute for Marine Sciences at the University of Kiel

==== Thesis ====

The type of a thesis.
* If the publication is a thesis, this field defines the type of academic degree.

Examples:

 diploma thesis
 Ph.D.thesis
 Doctoral thesis
 Habilitation thesis

==== Adress ====

The address and/or contact information of the author(s).
* Any info on how to contact the corresponding author(s) (often the first author of the paper), e.g. postal address of author institution, email address etc.).

Example:

 Granskog: Department of Geophysics, P.O. Box 64, FIN-00014 University of Helsinki, Finland, Email: mats@iki.fi;
 Meiners: Institute for Polar Ecology, University of Kiel, Wischhofstrasse 1-3, D-24148 Kiel, Germany

==== Keywords ====

The keywords given by the author.
* Contains keywords, as given in the article.
* Your personal keywords can be entered under "[[Adding_records#User Keys|User Keys]]".
* Multiple keywords should be separated by a semicolon (&lt;code&gt;;&lt;/code&gt;).

Examples:

 Baltic Sea; hydroacoustic; Sprat; Herring; GAM

==== Abstract ====

The abstract of this publication (if any) as given by the author.

==== Publisher ====

=== User fields (yellow fields) ===

==== User Keys ====

==== Marked &amp; Selected ====

* Both fields can be used to permanently "mark" (or "select") records so that one can easily come back to these records later on. It's up to you how you use these fields.
* The "selected" field is meant to indicate your "selected publications". This can be used to easily gather all publications of a particular author that shall be included on the institute's web site. Here's an example:

 [http://polaris.ipoe.uni-kiel.de/refs/show.php?author=piepenburg,%20d&amp;userID=4&amp;selected=yes&amp;submit=Cite&amp;showRows=100&amp;citeOrder=year&amp;headerMsg=Publications%20of%20**Dieter%20Piepenburg**: Publications of Dieter Piepenburg]

: In the above URL, note the use of the &lt;code&gt;&amp;selected=yes&lt;/code&gt; bit. I.e. the above URL displays all selected records that were authored by "D. Piepenburg" in Citation view (grouped by publication year), and adds a header message above the results list.

: For more info, please see how to setup dynamically updating [[Auto-updating_author/group_bibliographies|author (or group) bibliographies]].

[[Category:Usage]]
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<page arvcontinue="20231106215615|104">
  <title>Deleting records</title>
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    <model>wikitext</model>
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    <text bytes="1429" xml:space="preserve">In order to delete a record please click the little pencil (edit) icon that's available in any list view next to a record. Then press the "Delete Record" button at the bottom of the edit page.

The admin user is allowed to delete any records. A user, who is not logged in as admin, can remove an entry if all of the following conditions are met:

* user is logged in
* user is the owner/creator of this record (i.e., the user is the first one listed in the ''location'' field)
* nobody else is subscribed to this record (i.e., no other users are listed within the ''location'' field)
* user has permission to delete records (which is [[User permissions|set by the admin]])

When deleting a record, the information previously stored in the ''refs'' table of the database is not deleted but moved to the ''deleted'' table which obscures it from the web application. This allows an admin to recover accidentally deleted files (though, currently, no interface had been made to do this).

== Batch Deletion of Records ==

In the current version of refbase, there is no way to do a batch deletion of entries from within the web interface.
However, the admin can execute an [[Batch SQL modifications|appropriate MySQL command]] (via ''sql_search.php'') to remove many records at once.

PLEASE NOTE: in both cases, the uploaded and linked files (e.g. .pdf's) will not be deleted. So the admin should do this manually.

[[Category:Usage]]</text>
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    <model>wikitext</model>
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    <text bytes="1447" xml:space="preserve">In order to delete a record please click the little pencil (edit) icon that's available in any list view next to a record. Then press the "Delete Record" button at the bottom of the edit page.

The admin user is allowed to delete any records. A user, who is not logged in as admin, can remove an entry if all of the following conditions are met:

* user is logged in
* user is the owner/creator of this record (i.e., the user is the first one listed in the ''location'' field)
* nobody else is subscribed to this record (i.e., no other users are listed within the ''location'' field)
* user has permission to delete records (which is [[User permissions|set by the admin]])

When deleting a record, the information previously stored in the ''refs'' table of the database is not deleted but moved to the ''deleted'' table which obscures it from the web application. This allows an admin to recover accidentally deleted files (though, currently, no interface had been made to do this).

== Batch Deletion of Records ==

In the current version of refbase, there is no way to do a batch deletion of entries from within the web interface.
However, the admin can execute an [[Batch SQL modifications|appropriate MySQL command]] (via ''sql_search.php'') to remove many records at once.

PLEASE NOTE: in both cases, the uploaded and linked files (e.g. .pdf's) will not be deleted. So the admin should do this manually.

[[Category:Usage]]
__NOEDITSECTION__</text>
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    <minor/>
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    <model>wikitext</model>
    <format>text/x-wiki</format>
    <text bytes="1460" xml:space="preserve">In order to delete a record please click the little pencil (edit) icon that's available in any list view next to a record. Then press the "Delete Record" button at the bottom of the edit page.

The admin user is allowed to delete any records. A user, who is not logged in as admin, can remove an entry if all of the following conditions are met:

* user is logged in
* user is the owner/creator of this record (i.e., the user is the first one listed in the ''location'' field)
* nobody else is subscribed to this record (i.e., no other users are listed within the ''location'' field)
* user has permission to delete records (which is [[User permissions|set by the admin]])

When deleting a record, the information previously stored in the ''refs'' table of the database is not deleted but moved to the ''deleted'' table which obscures it from the web application. This allows an admin to recover accidentally deleted files. However, so far no interface has been made to do this.

== Batch Deletion of Records ==

In the current version of refbase, there is no way to do a batch deletion of entries from within the web interface.
However, the admin can execute an [[Batch SQL modifications|appropriate MySQL command]] (via ''sql_search.php'') to remove many records at once.

PLEASE NOTE: In both cases, the uploaded and linked files (e.g. .pdf's) will not be deleted. So the admin has to remove any related files manually.

[[Category:Usage]]
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<page arvcontinue="20231106215615|104">
  <title>Sharing records</title>
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    <text bytes="7873" xml:space="preserve">This document describes how to share records &amp; bibliographies among different users and answers sharing-related questions.

== Benefits of sharing your bibliographic records with other users ==

refbase was developed to allow different users to share the same pool of bibliographic records. By collaboratively working on the same bibliographic dataset, members of a research group can work more efficiently since it means less work for each individual group member. A shared reference database will also help everyone in the group to stay on top of the most recent literature. In addition, it allows you to build shared bibliographies and fulltext repositories for particular research topics, groups or authors.

== How can I share a record with others? ==

By default, a record is "owned" by the person who added or imported it. For each record, the name of the record's owner is listed at the beginning of the ''location'' field which is shown in details view (but can also be displayed in list view using the [[Display Options]] form). 

You can "subscribe" to an existing record (that's owned by somebody else) using these steps:

* Login to your refbase database.
* Find the record you'd like to add to your own library of records.
* Click the 'edit record' link (the little "pencil" icon) that's displayed next to your record.
* At the very bottom of the displayed editing form, choose ''''add''' my name &amp; email address' from the drop-down menu.
* Click the 'Save Changes' button.

&lt;div class="right-sidebar"&gt;[[image:SubscribeToRecord.jpg|thumb|How to add a record to your library]]&lt;/div&gt;

This will add the record to your own library, and the record will be returned when clicking the 'My Refs' link on any search results page. Note that your name will also be appended to the contents of that record's ''location'' field, which tells other users that this record belongs to your personal library of records.

== Can everybody view &amp; edit my own records? ==

Yes and no. refbase works similar to a [http://en.wikipedia.org/wiki/Wiki wiki] where every (logged-in) user is allowed to view &amp; edit the common fields of every database record. This is done to encourage collaboration and generally helps to improve the quality of your records ([[Editing records|more info]]). However, the admin is able to globally disallow editing for particular users and future versions may allow for record-specific access control (see [[#Future plans|below]]).

It's also worth noting that every user has a list of private fields (we call them user-specific fields) which are marked with a yellow background color. Since each user will only be able to view &amp; edit his own user-specific fields, you can rest assured that your input within these "yellow" fields will be kept private.

== How can I browse bibliographies of other users? ==

Want to see all records in the library of a particular user? This can be done by searching the ''location'' field for that user's name (or parts of it). The ''location'' field is availabe in [[Advanced Search]] as well as the [[Search within Results]] form that's displayed on any search results page. So, one way of displaying another user's entire library would be to click the 'Show All' link in the page header, then searching the ''location'' field for that user's name using the 'Search within Results' form. (see [[#Future plans|below]] for future plans regarding the browsing of other user's bibliographies)

As always, you can use the 'Search within Results' and 'Display Options' forms to further narrow down your search results and customize its display. If you've found some interesting records, you may want to subscribe to them (see [[#How can I share a record with others?|above]]) or add them to your personal groups. Also note that you can easily [[Recall My Query|save any search result set]] (including its current display settings) using the 'save' link in the page header. Results of any saved query can be easily recalled via the 'Recall My Query' form on the main page.

== How can I track literature on my research topic or from a particular author? ==

refbase offers several methods to discover newly added records that match a particular topic or author:

=== Links on main page ===

You can always checkout recently added records via any of the relevant links on the main page (added: today | yesterday | last 7 days | since last login), then use the 'Search within Results' functionality to find records that interest you. See below for more fine-tuned and/or automatic ways to stay on track with recent database additions.

=== Email notifications ===

The database admin can setup a mailing list for the purpose of refbase notifications. If you're subscribed to such a mailing list, refbase will let you know via email whenever a new record is added to the database. The email will contain the main bibliographic info of the newly added record as well as a direct link to its full record details in the database. A screenshot of such an email notification is available [http://refbase.sourceforge.net/features/EmailAnnouncement.html here]. Most current email clients will allow you to filter the refbase email notifications for particular topics or authors.

=== Saved queries ===

If you'd only like to see records matching a particular topic or author, you could perform a query for your desired search term(s), sort results by creation date and save the query using the 'save query' feature. Choosing again your saved query (via the 'Recall My Query' form on the main page) will always display all records matching your saved search terms, with newly added records being listed at the top of your search results list. An example for this method is given [[Recall My Query|here]].

=== Custom RSS feeds ===

refbase can generate RSS feeds from your searches. This allows you to use your RSS newsreader to track newly added records matching a certain topic or author. To do so, simply perform a query for your desired search term(s), then subscribe to the RSS feed that's available via the 'RSS' link in the page header above the search results list. ([[RSS features|more info]])

== How can I build shared bibliographies for particular research topics, groups or authors? ==

refbase allows you to construct links to automatically updating bibliographies of particular topics, groups or authors. These links can be included in your web pages, and users could subscribe to any of your shared bibliographies via RSS feeds. The feature is described in more detail (and with many examples) [[Linking to records#Displaying records of a particular author|here]] and [[Auto-updating author/group bibliographies|here]].

== Future plans ==

We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system. In addition, we'd like to implement a simple note taking system where multiple notes/comments could be attached to a particular record and which could also be made public, group-specific or private. ([[Planned feature additions#Sharing|more info]])

Future versions of refbase may also allow record owners to set fine-grained access control on record level. This would enable the record owner (or the admin) to specify who'll be permitted to view or edit a particular record (see our planned feature "[[Planned feature additions#Record-specific permissions|record-specific permissions]]").

With regard to browsing of other user's bibliographies, we have started to develop a generic "browse" feature which will make it easy to browse your refbase database by particular field values (such as authors, keywords, users, etc). This would give you easy access to the bibliographies of all database users directly from the main page.

[[Category:Usage]]</text>
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    <text bytes="7891" xml:space="preserve">This document describes how to share records &amp; bibliographies among different users and answers sharing-related questions.

== Benefits of sharing your bibliographic records with other users ==

refbase was developed to allow different users to share the same pool of bibliographic records. By collaboratively working on the same bibliographic dataset, members of a research group can work more efficiently since it means less work for each individual group member. A shared reference database will also help everyone in the group to stay on top of the most recent literature. In addition, it allows you to build shared bibliographies and fulltext repositories for particular research topics, groups or authors.

== How can I share a record with others? ==

By default, a record is "owned" by the person who added or imported it. For each record, the name of the record's owner is listed at the beginning of the ''location'' field which is shown in details view (but can also be displayed in list view using the [[Display Options]] form). 

You can "subscribe" to an existing record (that's owned by somebody else) using these steps:

* Login to your refbase database.
* Find the record you'd like to add to your own library of records.
* Click the 'edit record' link (the little "pencil" icon) that's displayed next to your record.
* At the very bottom of the displayed editing form, choose ''''add''' my name &amp; email address' from the drop-down menu.
* Click the 'Save Changes' button.

&lt;div class="right-sidebar"&gt;[[image:SubscribeToRecord.jpg|thumb|How to add a record to your library]]&lt;/div&gt;

This will add the record to your own library, and the record will be returned when clicking the 'My Refs' link on any search results page. Note that your name will also be appended to the contents of that record's ''location'' field, which tells other users that this record belongs to your personal library of records.

== Can everybody view &amp; edit my own records? ==

Yes and no. refbase works similar to a [http://en.wikipedia.org/wiki/Wiki wiki] where every (logged-in) user is allowed to view &amp; edit the common fields of every database record. This is done to encourage collaboration and generally helps to improve the quality of your records ([[Editing records|more info]]). However, the admin is able to globally disallow editing for particular users and future versions may allow for record-specific access control (see [[#Future plans|below]]).

It's also worth noting that every user has a list of private fields (we call them user-specific fields) which are marked with a yellow background color. Since each user will only be able to view &amp; edit his own user-specific fields, you can rest assured that your input within these "yellow" fields will be kept private.

== How can I browse bibliographies of other users? ==

Want to see all records in the library of a particular user? This can be done by searching the ''location'' field for that user's name (or parts of it). The ''location'' field is availabe in [[Advanced Search]] as well as the [[Search within Results]] form that's displayed on any search results page. So, one way of displaying another user's entire library would be to click the 'Show All' link in the page header, then searching the ''location'' field for that user's name using the 'Search within Results' form. (see [[#Future plans|below]] for future plans regarding the browsing of other user's bibliographies)

As always, you can use the 'Search within Results' and 'Display Options' forms to further narrow down your search results and customize its display. If you've found some interesting records, you may want to subscribe to them (see [[#How can I share a record with others?|above]]) or add them to your personal groups. Also note that you can easily [[Recall My Query|save any search result set]] (including its current display settings) using the 'save' link in the page header. Results of any saved query can be easily recalled via the 'Recall My Query' form on the main page.

== How can I track literature on my research topic or from a particular author? ==

refbase offers several methods to discover newly added records that match a particular topic or author:

=== Links on main page ===

You can always checkout recently added records via any of the relevant links on the main page (added: today | yesterday | last 7 days | since last login), then use the 'Search within Results' functionality to find records that interest you. See below for more fine-tuned and/or automatic ways to stay on track with recent database additions.

=== Email notifications ===

The database admin can setup a mailing list for the purpose of refbase notifications. If you're subscribed to such a mailing list, refbase will let you know via email whenever a new record is added to the database. The email will contain the main bibliographic info of the newly added record as well as a direct link to its full record details in the database. A screenshot of such an email notification is available [http://refbase.sourceforge.net/features/EmailAnnouncement.html here]. Most current email clients will allow you to filter the refbase email notifications for particular topics or authors.

=== Saved queries ===

If you'd only like to see records matching a particular topic or author, you could perform a query for your desired search term(s), sort results by creation date and save the query using the 'save query' feature. Choosing again your saved query (via the 'Recall My Query' form on the main page) will always display all records matching your saved search terms, with newly added records being listed at the top of your search results list. An example for this method is given [[Recall My Query|here]].

=== Custom RSS feeds ===

refbase can generate RSS feeds from your searches. This allows you to use your RSS newsreader to track newly added records matching a certain topic or author. To do so, simply perform a query for your desired search term(s), then subscribe to the RSS feed that's available via the 'RSS' link in the page header above the search results list. ([[RSS features|more info]])

== How can I build shared bibliographies for particular research topics, groups or authors? ==

refbase allows you to construct links to automatically updating bibliographies of particular topics, groups or authors. These links can be included in your web pages, and users could subscribe to any of your shared bibliographies via RSS feeds. The feature is described in more detail (and with many examples) [[Linking to records#Displaying records of a particular author|here]] and [[Auto-updating author/group bibliographies|here]].

== Future plans ==

We plan to open up the refbase group (aka tagging) mechanism so that groups can be made public, group-specific or private. This will enable users to share their groups with each other and establish a common categorization system. In addition, we'd like to implement a simple note taking system where multiple notes/comments could be attached to a particular record and which could also be made public, group-specific or private. ([[Planned feature additions#Sharing|more info]])

Future versions of refbase may also allow record owners to set fine-grained access control on record level. This would enable the record owner (or the admin) to specify who'll be permitted to view or edit a particular record (see our planned feature "[[Planned feature additions#Record-specific permissions|record-specific permissions]]").

With regard to browsing of other user's bibliographies, we have started to develop a generic "browse" feature which will make it easy to browse your refbase database by particular field values (such as authors, keywords, users, etc). This would give you easy access to the bibliographies of all database users directly from the main page.

[[Category:Usage]]
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